%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'>
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'
#
Monitor.sh calls M_MLD_2D
and AWTD.sh, Fluxnet.sh, Siconc.sh, IceClim.sh, FWC_SSH.sh
AWTD.sh M_AWTMD
Fluxnet.sh M_Fluxnet
FWC_SSH.sh M_FWC_2D M_FWC_integrals M_FWC_SSH M_SSH_anomaly
Integrals.sh 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= irene4604.c-irene.mg1.tgcc.ccc.cea.fr starting dask cluster on local= True workers 16 10000000000 False tgcc local cluster starting This code is running on irene4604.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= 01 outputpath= ../results/SEDNA_DELTA_MONITOR/ daskreport= ../results/dask/6419110irene4604.c-irene.mg1.tgcc.ccc.cea.fr_SEDNA_DELTA_MONITOR_01M_AWTMD/ CPU times: user 3.76 s, sys: 741 ms, total: 4.5 s Wall time: 1min 33s
Client-ec42dfc4-13d8-11ed-be3a-080038b9474d
Connection method: Cluster object | Cluster type: distributed.LocalCluster |
Dashboard: http://127.0.0.1:8787/status |
b4c53324
Dashboard: http://127.0.0.1:8787/status | Workers: 64 |
Total threads: 256 | Total memory: 251.06 GiB |
Status: running | Using processes: True |
Scheduler-848add83-1f56-408b-b081-537ce6a36d13
Comm: tcp://127.0.0.1:33368 | Workers: 64 |
Dashboard: http://127.0.0.1:8787/status | Total threads: 256 |
Started: 1 minute ago | Total memory: 251.06 GiB |
Comm: tcp://127.0.0.1:33076 | Total threads: 4 |
Dashboard: http://127.0.0.1:42568/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:36906 | |
Local directory: /tmp/dask-worker-space/worker-5erg1uzh |
Comm: tcp://127.0.0.1:44402 | Total threads: 4 |
Dashboard: http://127.0.0.1:41747/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:35118 | |
Local directory: /tmp/dask-worker-space/worker-fp1q5c72 |
Comm: tcp://127.0.0.1:42439 | Total threads: 4 |
Dashboard: http://127.0.0.1:38039/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:45380 | |
Local directory: /tmp/dask-worker-space/worker-25_cmehr |
Comm: tcp://127.0.0.1:38040 | Total threads: 4 |
Dashboard: http://127.0.0.1:40638/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:42929 | |
Local directory: /tmp/dask-worker-space/worker-wtv8zc9a |
Comm: tcp://127.0.0.1:34351 | Total threads: 4 |
Dashboard: http://127.0.0.1:44811/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:33027 | |
Local directory: /tmp/dask-worker-space/worker-wi9feq6a |
Comm: tcp://127.0.0.1:34749 | Total threads: 4 |
Dashboard: http://127.0.0.1:37416/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:34502 | |
Local directory: /tmp/dask-worker-space/worker-oyx6vdx9 |
Comm: tcp://127.0.0.1:44569 | Total threads: 4 |
Dashboard: http://127.0.0.1:45900/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:43612 | |
Local directory: /tmp/dask-worker-space/worker-i290y6uf |
Comm: tcp://127.0.0.1:46813 | Total threads: 4 |
Dashboard: http://127.0.0.1:44805/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:36061 | |
Local directory: /tmp/dask-worker-space/worker-g67khqiz |
Comm: tcp://127.0.0.1:45839 | Total threads: 4 |
Dashboard: http://127.0.0.1:46566/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:35747 | |
Local directory: /tmp/dask-worker-space/worker-7f0m7rzx |
Comm: tcp://127.0.0.1:37616 | Total threads: 4 |
Dashboard: http://127.0.0.1:45107/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:37927 | |
Local directory: /tmp/dask-worker-space/worker-li500pm1 |
Comm: tcp://127.0.0.1:37518 | Total threads: 4 |
Dashboard: http://127.0.0.1:33838/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:42263 | |
Local directory: /tmp/dask-worker-space/worker-9mlgyzdc |
Comm: tcp://127.0.0.1:44081 | Total threads: 4 |
Dashboard: http://127.0.0.1:37795/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:34806 | |
Local directory: /tmp/dask-worker-space/worker-d1acoji2 |
Comm: tcp://127.0.0.1:34090 | Total threads: 4 |
Dashboard: http://127.0.0.1:38132/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:34255 | |
Local directory: /tmp/dask-worker-space/worker-8tei1qel |
Comm: tcp://127.0.0.1:33566 | Total threads: 4 |
Dashboard: http://127.0.0.1:43002/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:33292 | |
Local directory: /tmp/dask-worker-space/worker-j18wv0ck |
Comm: tcp://127.0.0.1:37718 | Total threads: 4 |
Dashboard: http://127.0.0.1:42669/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:40329 | |
Local directory: /tmp/dask-worker-space/worker-8xci732t |
Comm: tcp://127.0.0.1:33828 | Total threads: 4 |
Dashboard: http://127.0.0.1:44540/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:45955 | |
Local directory: /tmp/dask-worker-space/worker-qd8hip7t |
Comm: tcp://127.0.0.1:37558 | Total threads: 4 |
Dashboard: http://127.0.0.1:35059/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:42406 | |
Local directory: /tmp/dask-worker-space/worker-blniqljk |
Comm: tcp://127.0.0.1:33918 | Total threads: 4 |
Dashboard: http://127.0.0.1:43762/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:38693 | |
Local directory: /tmp/dask-worker-space/worker-8s2rucbs |
Comm: tcp://127.0.0.1:45103 | Total threads: 4 |
Dashboard: http://127.0.0.1:42860/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:36673 | |
Local directory: /tmp/dask-worker-space/worker-d8fi5nzi |
Comm: tcp://127.0.0.1:38319 | Total threads: 4 |
Dashboard: http://127.0.0.1:33880/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:34997 | |
Local directory: /tmp/dask-worker-space/worker-0ubbwnkw |
Comm: tcp://127.0.0.1:35708 | Total threads: 4 |
Dashboard: http://127.0.0.1:33417/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:40389 | |
Local directory: /tmp/dask-worker-space/worker-egs97s2j |
Comm: tcp://127.0.0.1:34256 | Total threads: 4 |
Dashboard: http://127.0.0.1:33602/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:34411 | |
Local directory: /tmp/dask-worker-space/worker-8subw54e |
Comm: tcp://127.0.0.1:45816 | Total threads: 4 |
Dashboard: http://127.0.0.1:44330/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:33815 | |
Local directory: /tmp/dask-worker-space/worker-iihlewp_ |
Comm: tcp://127.0.0.1:46122 | Total threads: 4 |
Dashboard: http://127.0.0.1:42993/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:33544 | |
Local directory: /tmp/dask-worker-space/worker-cyb9mf5g |
Comm: tcp://127.0.0.1:33744 | Total threads: 4 |
Dashboard: http://127.0.0.1:37658/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:37618 | |
Local directory: /tmp/dask-worker-space/worker-rjqsoxk3 |
Comm: tcp://127.0.0.1:46506 | Total threads: 4 |
Dashboard: http://127.0.0.1:46060/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:38854 | |
Local directory: /tmp/dask-worker-space/worker-t0miru_i |
Comm: tcp://127.0.0.1:39693 | Total threads: 4 |
Dashboard: http://127.0.0.1:39063/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:38457 | |
Local directory: /tmp/dask-worker-space/worker-cp5sxm67 |
Comm: tcp://127.0.0.1:42161 | Total threads: 4 |
Dashboard: http://127.0.0.1:41699/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:35297 | |
Local directory: /tmp/dask-worker-space/worker-0i701k0i |
Comm: tcp://127.0.0.1:35523 | Total threads: 4 |
Dashboard: http://127.0.0.1:38871/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:39278 | |
Local directory: /tmp/dask-worker-space/worker-_bset0zh |
Comm: tcp://127.0.0.1:34210 | Total threads: 4 |
Dashboard: http://127.0.0.1:33537/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:42082 | |
Local directory: /tmp/dask-worker-space/worker-x3kvblpt |
Comm: tcp://127.0.0.1:42450 | Total threads: 4 |
Dashboard: http://127.0.0.1:36088/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:36988 | |
Local directory: /tmp/dask-worker-space/worker-_tb6lfrp |
Comm: tcp://127.0.0.1:34538 | Total threads: 4 |
Dashboard: http://127.0.0.1:45799/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:33152 | |
Local directory: /tmp/dask-worker-space/worker-16qg7bgc |
Comm: tcp://127.0.0.1:46676 | Total threads: 4 |
Dashboard: http://127.0.0.1:35503/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:42545 | |
Local directory: /tmp/dask-worker-space/worker-xejux_js |
Comm: tcp://127.0.0.1:41707 | Total threads: 4 |
Dashboard: http://127.0.0.1:44738/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:44316 | |
Local directory: /tmp/dask-worker-space/worker-s4857g1o |
Comm: tcp://127.0.0.1:42632 | Total threads: 4 |
Dashboard: http://127.0.0.1:38544/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:41001 | |
Local directory: /tmp/dask-worker-space/worker-o079w5ba |
Comm: tcp://127.0.0.1:32997 | Total threads: 4 |
Dashboard: http://127.0.0.1:34193/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:36099 | |
Local directory: /tmp/dask-worker-space/worker-xh1z3861 |
Comm: tcp://127.0.0.1:35811 | Total threads: 4 |
Dashboard: http://127.0.0.1:33279/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:45802 | |
Local directory: /tmp/dask-worker-space/worker-9cx4a2or |
Comm: tcp://127.0.0.1:33899 | Total threads: 4 |
Dashboard: http://127.0.0.1:34204/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:46238 | |
Local directory: /tmp/dask-worker-space/worker-mdzg8wf3 |
Comm: tcp://127.0.0.1:35173 | Total threads: 4 |
Dashboard: http://127.0.0.1:33950/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:39400 | |
Local directory: /tmp/dask-worker-space/worker-gqxsavdw |
Comm: tcp://127.0.0.1:36751 | Total threads: 4 |
Dashboard: http://127.0.0.1:39456/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:38139 | |
Local directory: /tmp/dask-worker-space/worker-osorcjrf |
Comm: tcp://127.0.0.1:40973 | Total threads: 4 |
Dashboard: http://127.0.0.1:38234/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:39766 | |
Local directory: /tmp/dask-worker-space/worker-tu9yppjk |
Comm: tcp://127.0.0.1:34486 | Total threads: 4 |
Dashboard: http://127.0.0.1:38066/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:46521 | |
Local directory: /tmp/dask-worker-space/worker-3fgpf4xf |
Comm: tcp://127.0.0.1:42466 | Total threads: 4 |
Dashboard: http://127.0.0.1:36182/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:36590 | |
Local directory: /tmp/dask-worker-space/worker-0a6frhsm |
Comm: tcp://127.0.0.1:38002 | Total threads: 4 |
Dashboard: http://127.0.0.1:33962/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:33913 | |
Local directory: /tmp/dask-worker-space/worker-ct20fqlj |
Comm: tcp://127.0.0.1:41528 | Total threads: 4 |
Dashboard: http://127.0.0.1:32959/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:41487 | |
Local directory: /tmp/dask-worker-space/worker-hm7krr3m |
Comm: tcp://127.0.0.1:37786 | Total threads: 4 |
Dashboard: http://127.0.0.1:41374/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:39909 | |
Local directory: /tmp/dask-worker-space/worker-ehi9z6se |
Comm: tcp://127.0.0.1:38627 | Total threads: 4 |
Dashboard: http://127.0.0.1:33249/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:39324 | |
Local directory: /tmp/dask-worker-space/worker-rwu_ezag |
Comm: tcp://127.0.0.1:40972 | Total threads: 4 |
Dashboard: http://127.0.0.1:44067/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:38044 | |
Local directory: /tmp/dask-worker-space/worker-lnn8g2jb |
Comm: tcp://127.0.0.1:40527 | Total threads: 4 |
Dashboard: http://127.0.0.1:37391/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:37843 | |
Local directory: /tmp/dask-worker-space/worker-2ytadab8 |
Comm: tcp://127.0.0.1:46614 | Total threads: 4 |
Dashboard: http://127.0.0.1:37109/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:32771 | |
Local directory: /tmp/dask-worker-space/worker-iqu8u98l |
Comm: tcp://127.0.0.1:34371 | Total threads: 4 |
Dashboard: http://127.0.0.1:37717/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:36951 | |
Local directory: /tmp/dask-worker-space/worker-yj0edgi3 |
Comm: tcp://127.0.0.1:38191 | Total threads: 4 |
Dashboard: http://127.0.0.1:34734/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:35847 | |
Local directory: /tmp/dask-worker-space/worker-4a3bzcge |
Comm: tcp://127.0.0.1:45336 | Total threads: 4 |
Dashboard: http://127.0.0.1:38606/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:43277 | |
Local directory: /tmp/dask-worker-space/worker-k7mxs5_f |
Comm: tcp://127.0.0.1:34850 | Total threads: 4 |
Dashboard: http://127.0.0.1:36482/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:43590 | |
Local directory: /tmp/dask-worker-space/worker-gtuqyam3 |
Comm: tcp://127.0.0.1:44988 | Total threads: 4 |
Dashboard: http://127.0.0.1:44584/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:43844 | |
Local directory: /tmp/dask-worker-space/worker-6qht5_l7 |
Comm: tcp://127.0.0.1:33008 | Total threads: 4 |
Dashboard: http://127.0.0.1:33505/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:39620 | |
Local directory: /tmp/dask-worker-space/worker-xgwzgfqm |
Comm: tcp://127.0.0.1:42810 | Total threads: 4 |
Dashboard: http://127.0.0.1:42345/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:45452 | |
Local directory: /tmp/dask-worker-space/worker-o5er5aim |
Comm: tcp://127.0.0.1:37871 | Total threads: 4 |
Dashboard: http://127.0.0.1:42546/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:40848 | |
Local directory: /tmp/dask-worker-space/worker-kgwpq54e |
Comm: tcp://127.0.0.1:35543 | Total threads: 4 |
Dashboard: http://127.0.0.1:33862/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:39395 | |
Local directory: /tmp/dask-worker-space/worker-uqdnl3g4 |
Comm: tcp://127.0.0.1:44168 | Total threads: 4 |
Dashboard: http://127.0.0.1:40586/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:35586 | |
Local directory: /tmp/dask-worker-space/worker-he6dwlp4 |
Comm: tcp://127.0.0.1:34424 | Total threads: 4 |
Dashboard: http://127.0.0.1:35893/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:46426 | |
Local directory: /tmp/dask-worker-space/worker-tvgv9pci |
Comm: tcp://127.0.0.1:41680 | Total threads: 4 |
Dashboard: http://127.0.0.1:42685/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:44746 | |
Local directory: /tmp/dask-worker-space/worker-fz8m6juw |
Comm: tcp://127.0.0.1:45446 | Total threads: 4 |
Dashboard: http://127.0.0.1:43445/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:40526 | |
Local directory: /tmp/dask-worker-space/worker-fr735bdo |
Comm: tcp://127.0.0.1:36097 | Total threads: 4 |
Dashboard: http://127.0.0.1:45161/status | Memory: 3.92 GiB |
Nanny: tcp://127.0.0.1:42875 | |
Local directory: /tmp/dask-worker-space/worker-gspro31m |
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 | |
---|---|---|---|---|---|---|---|---|---|---|
AW_maxtemp_depth | gridT.votemper,gridS.vosaline,param.mask,param... | calc.AWTD4(data) | ALL | AWTD_map | jet | (0,800) | m | M-5 |
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 True lazy= False ../lib/SEDNA_DELTA_MONITOR.yaml using param_xios reading ../lib/SEDNA_DELTA_MONITOR.yaml using param_xios reading <bound method DataSourceBase.describe of sources: param_xios: args: combine: nested concat_dim: y urlpath: /ccc/work/cont003/gen7420/odakatin/CONFIGS/SEDNA/SEDNA-I/SEDNA_Domain_cfg_Tgt_20210423_tsh10m_L1/param_f32/x_*.nc xarray_kwargs: compat: override coords: minimal data_vars: minimal parallel: true description: SEDNA NEMO parameters from MPI output nav_lon lat fails driver: intake_xarray.netcdf.NetCDFSource metadata: catalog_dir: /ccc/work/cont003/gen7420/odakatin/monitor-sedna/notebook/../lib/ > {'name': 'param_xios', 'container': 'xarray', 'plugin': ['netcdf'], 'driver': ['netcdf'], 'description': 'SEDNA NEMO parameters from MPI output nav_lon lat fails', 'direct_access': 'forbid', 'user_parameters': [{'name': 'path', 'description': 'file coordinate', 'type': 'str', 'default': '/ccc/work/cont003/gen7420/odakatin/CONFIGS/SEDNA/MESH/SEDNA_mesh_mask_Tgt_20210423_tsh10m_L1/param'}], 'metadata': {}, 'args': {'urlpath': '/ccc/work/cont003/gen7420/odakatin/CONFIGS/SEDNA/SEDNA-I/SEDNA_Domain_cfg_Tgt_20210423_tsh10m_L1/param_f32/x_*.nc', 'combine': 'nested', 'concat_dim': 'y'}} 0 read gridS ['vosaline'] lazy= False using load_data_xios_kerchunk reading gridS using load_data_xios_kerchunk reading <bound method DataSourceBase.describe of sources: data_xios_kerchunk: args: consolidated: false storage_options: fo: file:////ccc/cont003/home/ra5563/ra5563/catalogue/DELTA/201201/gridS_0[0-5][0-9][0-9].json target_protocol: file urlpath: reference:// description: CREG025 NEMO outputs from different xios server in kerchunk format driver: intake_xarray.xzarr.ZarrSource metadata: catalog_dir: /ccc/work/cont003/gen7420/odakatin/monitor-sedna/notebook/../lib/ > took 35.775102615356445 seconds 0 merging gridS ['vosaline'] 1 read gridT ['votemper'] lazy= False using load_data_xios_kerchunk reading gridT using load_data_xios_kerchunk reading <bound method DataSourceBase.describe of sources: data_xios_kerchunk: args: consolidated: false storage_options: fo: file:////ccc/cont003/home/ra5563/ra5563/catalogue/DELTA/201201/gridT_0[0-5][0-9][0-9].json target_protocol: file urlpath: reference:// description: CREG025 NEMO outputs from different xios server in kerchunk format driver: intake_xarray.xzarr.ZarrSource metadata: catalog_dir: /ccc/work/cont003/gen7420/odakatin/monitor-sedna/notebook/../lib/ > took 36.24394702911377 seconds 1 merging gridT ['votemper'] took 0.8498268127441406 seconds param mask2d will be included in data param nav_lat will be included in data param nav_lon will be included in data param mask will be included in data param depth will be included in data CPU times: user 49.9 s, sys: 14.2 s, total: 1min 4s Wall time: 2min 7s
<xarray.Dataset> Dimensions: (t: 31, z: 150, y: 6540, x: 6560) Coordinates: time_centered (t) object dask.array<chunksize=(1,), meta=np.ndarray> * t (t) object 2012-01-01 12:00:00 ... 2012-01-31 12:00:00 * y (y) int64 1 2 3 4 5 6 7 ... 6535 6536 6537 6538 6539 6540 * x (x) int64 1 2 3 4 5 6 7 ... 6555 6556 6557 6558 6559 6560 * z (z) int64 1 2 3 4 5 6 7 8 ... 143 144 145 146 147 148 149 150 mask2d (y, x) bool dask.array<chunksize=(13, 6560), meta=np.ndarray> nav_lat (y, x) float32 dask.array<chunksize=(13, 6560), meta=np.ndarray> nav_lon (y, x) float32 dask.array<chunksize=(13, 6560), meta=np.ndarray> mask (z, y, x) bool dask.array<chunksize=(150, 13, 6560), meta=np.ndarray> depth (z, y, x) float32 dask.array<chunksize=(150, 13, 6560), meta=np.ndarray> Data variables: vosaline (t, z, y, x) float32 dask.array<chunksize=(1, 150, 13, 6560), meta=np.ndarray> votemper (t, z, y, x) float32 dask.array<chunksize=(1, 150, 13, 6560), 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
%%time
monitor.auto(df,data,savefig,daskreport,outputpath,file_exp='SEDNA'
)
#calc= True #save= True #plot= False Value='AW_maxtemp_depth' Zone='ALL' Plot='AWTD_map' cmap='jet' clabel='m' clim= (0, 800) outputpath='../results/SEDNA_DELTA_MONITOR/' nc_outputpath='../nc_results/SEDNA_DELTA_MONITOR/' filename='SEDNA_AWTD_map_ALL_AW_maxtemp_depth' data=monitor.optimize_dataset(data) #3 Start computing data= calc.AWTD4(data) monitor.optimize_dataset(data) add optimise here once otimise can recognise
<xarray.Dataset> Dimensions: (t: 31, y: 6540, x: 6560) Coordinates: time_centered (t) object dask.array<chunksize=(1,), meta=np.ndarray> * t (t) object 2012-01-01 12:00:00 ... 2012-01-31 12:00:00 * y (y) int64 1 2 3 4 5 6 7 ... 6535 6536 6537 6538 6539 6540 * x (x) int64 1 2 3 4 5 6 7 ... 6555 6556 6557 6558 6559 6560 mask2d (y, x) bool dask.array<chunksize=(13, 6560), meta=np.ndarray> nav_lat (y, x) float32 dask.array<chunksize=(13, 6560), meta=np.ndarray> nav_lon (y, x) float32 dask.array<chunksize=(13, 6560), meta=np.ndarray> Data variables: AWT (t, y, x) float32 dask.array<chunksize=(1, 13, 6560), meta=np.ndarray> AWD (t, y, x) float32 dask.array<chunksize=(1, 13, 6560), meta=np.ndarray>
#4 Saving SEDNA_AWTD_map_ALL_AW_maxtemp_depth data=save.datas(data,plot=Plot,path=nc_outputpath,filename=filename) start saving data saving data in a file t (1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 slice(0, 1, None)
/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) 2022-08-04 11:42:09,376 - distributed.worker - ERROR - Worker stream died during communication: tcp://127.0.0.1:44081 Traceback (most recent call last): File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/comm/tcp.py", line 264, in write async def write(self, msg, serializers=None, on_error="message"): asyncio.exceptions.CancelledError During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/asyncio/tasks.py", line 418, in wait_for return fut.result() asyncio.exceptions.CancelledError The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/comm/core.py", line 329, in connect await asyncio.wait_for(comm.write(local_info), time_left()) File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/asyncio/tasks.py", line 420, in wait_for raise exceptions.TimeoutError() from exc asyncio.exceptions.TimeoutError The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/worker.py", line 1983, in gather_dep response = await get_data_from_worker( File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/worker.py", line 2725, in get_data_from_worker return await retry_operation(_get_data, operation="get_data_from_worker") File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/utils_comm.py", line 383, in retry_operation return await retry( File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/utils_comm.py", line 368, in retry return await coro() File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/worker.py", line 2702, in _get_data comm = await rpc.connect(worker) File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/core.py", line 1371, in connect return await connect_attempt File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/core.py", line 1307, in _connect comm = await connect( File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/comm/core.py", line 333, in connect raise OSError( OSError: Timed out during handshake while connecting to tcp://127.0.0.1:44081 after 30 s /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) 2022-08-04 11:42:09,903 - distributed.worker - ERROR - Worker stream died during communication: tcp://127.0.0.1:34486 Traceback (most recent call last): File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/comm/tcp.py", line 264, in write async def write(self, msg, serializers=None, on_error="message"): asyncio.exceptions.CancelledError During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/asyncio/tasks.py", line 418, in wait_for return fut.result() asyncio.exceptions.CancelledError The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/comm/core.py", line 329, in connect await asyncio.wait_for(comm.write(local_info), time_left()) File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/asyncio/tasks.py", line 420, in wait_for raise exceptions.TimeoutError() from exc asyncio.exceptions.TimeoutError The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/worker.py", line 1983, in gather_dep response = await get_data_from_worker( File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/worker.py", line 2725, in get_data_from_worker return await retry_operation(_get_data, operation="get_data_from_worker") File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/utils_comm.py", line 383, in retry_operation return await retry( File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/utils_comm.py", line 368, in retry return await coro() File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/worker.py", line 2702, in _get_data comm = await rpc.connect(worker) File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/core.py", line 1371, in connect return await connect_attempt File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/core.py", line 1307, in _connect comm = await connect( File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/comm/core.py", line 333, in connect raise OSError( OSError: Timed out during handshake while connecting to tcp://127.0.0.1:34486 after 30 s /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) 2022-08-04 11:42:10,145 - distributed.worker - ERROR - Worker stream died during communication: tcp://127.0.0.1:46614 Traceback (most recent call last): File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/comm/tcp.py", line 264, in write async def write(self, msg, serializers=None, on_error="message"): asyncio.exceptions.CancelledError During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/asyncio/tasks.py", line 418, in wait_for return fut.result() asyncio.exceptions.CancelledError The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/comm/core.py", line 329, in connect await asyncio.wait_for(comm.write(local_info), time_left()) File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/asyncio/tasks.py", line 420, in wait_for raise exceptions.TimeoutError() from exc asyncio.exceptions.TimeoutError The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/worker.py", line 1983, in gather_dep response = await get_data_from_worker( File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/worker.py", line 2725, in get_data_from_worker return await retry_operation(_get_data, operation="get_data_from_worker") File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/utils_comm.py", line 383, in retry_operation return await retry( File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/utils_comm.py", line 368, in retry return await coro() File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/worker.py", line 2702, in _get_data comm = await rpc.connect(worker) File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/core.py", line 1371, in connect return await connect_attempt File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/core.py", line 1307, in _connect comm = await connect( File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/comm/core.py", line 333, in connect raise OSError( OSError: Timed out during handshake while connecting to tcp://127.0.0.1:46614 after 30 s /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) 2022-08-04 11:42:11,147 - distributed.worker - ERROR - Worker stream died during communication: tcp://127.0.0.1:44988 Traceback (most recent call last): File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/comm/tcp.py", line 264, in write async def write(self, msg, serializers=None, on_error="message"): asyncio.exceptions.CancelledError During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/asyncio/tasks.py", line 418, in wait_for return fut.result() asyncio.exceptions.CancelledError The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/comm/core.py", line 329, in connect await asyncio.wait_for(comm.write(local_info), time_left()) File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/asyncio/tasks.py", line 420, in wait_for raise exceptions.TimeoutError() from exc asyncio.exceptions.TimeoutError The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/worker.py", line 1983, in gather_dep response = await get_data_from_worker( File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/worker.py", line 2725, in get_data_from_worker return await retry_operation(_get_data, operation="get_data_from_worker") File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/utils_comm.py", line 383, in retry_operation return await retry( File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/utils_comm.py", line 368, in retry return await coro() File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/worker.py", line 2702, in _get_data comm = await rpc.connect(worker) File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/core.py", line 1371, in connect return await connect_attempt File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/core.py", line 1307, in _connect comm = await connect( File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/comm/core.py", line 333, in connect raise OSError( OSError: Timed out during handshake while connecting to tcp://127.0.0.1:44988 after 30 s /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims)
slice(1, 2, None)
/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims)
slice(2, 3, None)
/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims) /ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims)
slice(3, 4, None) slice(4, 5, None)
/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/dask/array/reductions.py:608: RuntimeWarning: All-NaN slice encountered return np.nanmax(x_chunk, axis=axis, keepdims=keepdims)
slice(5, 6, None) slice(6, 7, None) slice(7, 8, None) slice(8, 9, None) slice(9, 10, None) slice(10, 11, None) slice(11, 12, None) slice(12, 13, None) slice(13, 14, None) slice(14, 15, None)
2022-08-04 11:48:29,091 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%)
slice(15, 16, None)
2022-08-04 11:48:40,257 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 11:48:43,244 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 11:48:54,996 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%)
slice(16, 17, None)
2022-08-04 11:49:06,541 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 11:49:09,611 - distributed.utils_perf - WARNING - full garbage collections took 10% CPU time recently (threshold: 10%) 2022-08-04 11:49:19,526 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%)
slice(17, 18, None)
2022-08-04 11:49:32,508 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 11:49:35,558 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 11:49:44,689 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%)
slice(18, 19, None)
2022-08-04 11:49:57,690 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 11:50:00,712 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 11:50:09,388 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%)
slice(19, 20, None)
2022-08-04 11:50:23,256 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 11:50:26,454 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 11:50:33,984 - distributed.utils_perf - WARNING - full garbage collections took 12% CPU time recently (threshold: 10%)
slice(20, 21, None)
2022-08-04 11:50:48,929 - distributed.utils_perf - WARNING - full garbage collections took 12% CPU time recently (threshold: 10%) 2022-08-04 11:50:52,022 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 11:50:58,923 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%)
slice(21, 22, None)
2022-08-04 11:51:15,192 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 11:51:18,573 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 11:51:21,513 - distributed.utils_perf - WARNING - full garbage collections took 12% CPU time recently (threshold: 10%)
slice(22, 23, None)
2022-08-04 11:51:39,277 - distributed.utils_perf - WARNING - full garbage collections took 12% CPU time recently (threshold: 10%) 2022-08-04 11:51:45,327 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 11:51:47,249 - distributed.utils_perf - WARNING - full garbage collections took 12% CPU time recently (threshold: 10%)
slice(23, 24, None)
2022-08-04 11:52:02,580 - distributed.utils_perf - WARNING - full garbage collections took 12% CPU time recently (threshold: 10%) 2022-08-04 11:52:10,858 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 11:52:12,654 - distributed.utils_perf - WARNING - full garbage collections took 12% CPU time recently (threshold: 10%) 2022-08-04 11:52:27,523 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%)
slice(24, 25, None)
2022-08-04 11:52:35,349 - distributed.utils_perf - WARNING - full garbage collections took 12% CPU time recently (threshold: 10%) 2022-08-04 11:52:38,134 - distributed.utils_perf - WARNING - full garbage collections took 12% CPU time recently (threshold: 10%) 2022-08-04 11:52:52,877 - distributed.utils_perf - WARNING - full garbage collections took 12% CPU time recently (threshold: 10%)
slice(25, 26, None)
2022-08-04 11:53:02,853 - distributed.utils_perf - WARNING - full garbage collections took 12% CPU time recently (threshold: 10%) 2022-08-04 11:53:04,776 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 11:53:20,886 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%)
slice(26, 27, None)
2022-08-04 11:53:29,235 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 11:53:31,936 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 11:53:46,630 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%)
slice(27, 28, None)
2022-08-04 11:53:55,043 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 11:53:57,689 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 11:54:12,401 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%)
slice(28, 29, None)
2022-08-04 11:54:20,790 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 11:54:23,594 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 11:54:40,528 - distributed.utils_perf - WARNING - full garbage collections took 10% CPU time recently (threshold: 10%)
slice(29, 30, None)
2022-08-04 11:54:48,282 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 11:54:51,531 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 11:55:04,839 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%)
slice(30, 31, None)
2022-08-04 11:55:13,913 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 11:55:16,780 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 11:55:33,759 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%)
CPU times: user 11min 59s, sys: 2min 14s, total: 14min 13s Wall time: 16min 59s