%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= irene5709.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 irene5709.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= 03 outputpath= ../results/SEDNA_DELTA_MONITOR/ daskreport= ../results/dask/6419595irene5709.c-irene.mg1.tgcc.ccc.cea.fr_SEDNA_DELTA_MONITOR_03M_AWTMD/ CPU times: user 477 ms, sys: 125 ms, total: 602 ms Wall time: 21.6 s
Client-501252db-13e4-11ed-8e9b-080038b93555
Connection method: Cluster object | Cluster type: distributed.LocalCluster |
Dashboard: http://127.0.0.1:8787/status |
b84daa3c
Dashboard: http://127.0.0.1:8787/status | Workers: 16 |
Total threads: 128 | Total memory: 251.06 GiB |
Status: running | Using processes: True |
Scheduler-640f3bb9-0544-4561-843d-2a8e7bc39ccd
Comm: tcp://127.0.0.1:38894 | Workers: 16 |
Dashboard: http://127.0.0.1:8787/status | Total threads: 128 |
Started: Just now | Total memory: 251.06 GiB |
Comm: tcp://127.0.0.1:32802 | Total threads: 8 |
Dashboard: http://127.0.0.1:38578/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:43754 | |
Local directory: /tmp/dask-worker-space/worker-fatok14p |
Comm: tcp://127.0.0.1:41898 | Total threads: 8 |
Dashboard: http://127.0.0.1:37874/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:34107 | |
Local directory: /tmp/dask-worker-space/worker-7mvbzpg5 |
Comm: tcp://127.0.0.1:41581 | Total threads: 8 |
Dashboard: http://127.0.0.1:40530/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:44991 | |
Local directory: /tmp/dask-worker-space/worker-186uw395 |
Comm: tcp://127.0.0.1:40830 | Total threads: 8 |
Dashboard: http://127.0.0.1:34178/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:44070 | |
Local directory: /tmp/dask-worker-space/worker-5p6ofm20 |
Comm: tcp://127.0.0.1:43430 | Total threads: 8 |
Dashboard: http://127.0.0.1:43816/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:34306 | |
Local directory: /tmp/dask-worker-space/worker-s46emh6g |
Comm: tcp://127.0.0.1:33227 | Total threads: 8 |
Dashboard: http://127.0.0.1:37357/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:33956 | |
Local directory: /tmp/dask-worker-space/worker-aw_ovg7d |
Comm: tcp://127.0.0.1:43729 | Total threads: 8 |
Dashboard: http://127.0.0.1:38263/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:36267 | |
Local directory: /tmp/dask-worker-space/worker-0v3ys8l5 |
Comm: tcp://127.0.0.1:46369 | Total threads: 8 |
Dashboard: http://127.0.0.1:43133/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:37656 | |
Local directory: /tmp/dask-worker-space/worker-zndo_odr |
Comm: tcp://127.0.0.1:45340 | Total threads: 8 |
Dashboard: http://127.0.0.1:41404/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:45539 | |
Local directory: /tmp/dask-worker-space/worker-oxmg49dv |
Comm: tcp://127.0.0.1:36763 | Total threads: 8 |
Dashboard: http://127.0.0.1:37711/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:43307 | |
Local directory: /tmp/dask-worker-space/worker-akl2mfx3 |
Comm: tcp://127.0.0.1:36483 | Total threads: 8 |
Dashboard: http://127.0.0.1:40991/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:45473 | |
Local directory: /tmp/dask-worker-space/worker-q2h2k2f8 |
Comm: tcp://127.0.0.1:45587 | Total threads: 8 |
Dashboard: http://127.0.0.1:36223/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:34536 | |
Local directory: /tmp/dask-worker-space/worker-rp32ul38 |
Comm: tcp://127.0.0.1:34256 | Total threads: 8 |
Dashboard: http://127.0.0.1:34403/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:41752 | |
Local directory: /tmp/dask-worker-space/worker-0l9c0n3d |
Comm: tcp://127.0.0.1:44359 | Total threads: 8 |
Dashboard: http://127.0.0.1:42951/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:40780 | |
Local directory: /tmp/dask-worker-space/worker-s6gvo0yx |
Comm: tcp://127.0.0.1:33305 | Total threads: 8 |
Dashboard: http://127.0.0.1:43148/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:41467 | |
Local directory: /tmp/dask-worker-space/worker-o9noqo6a |
Comm: tcp://127.0.0.1:37727 | Total threads: 8 |
Dashboard: http://127.0.0.1:33532/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:35793 | |
Local directory: /tmp/dask-worker-space/worker-m5h9u93o |
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/201203/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 45.14392948150635 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/201203/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 44.39779043197632 seconds 1 merging gridT ['votemper'] took 0.7860651016235352 seconds param depth will be included in data param nav_lat will be included in data param mask will be included in data param nav_lon will be included in data param mask2d will be included in data CPU times: user 38.2 s, sys: 5.76 s, total: 44 s Wall time: 1min 52s
<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 2012-03-01 12:00:00 ... 2012-03-31 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 depth (z, y, x) float32 dask.array<chunksize=(150, 13, 6560), meta=np.ndarray> nav_lat (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> nav_lon (y, x) float32 dask.array<chunksize=(13, 6560), meta=np.ndarray> mask2d (y, x) bool dask.array<chunksize=(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-19 12:40:34 GMT title: ocean T grid variables uuid: b2000bef-0e1f-4f0d-ae2a-b9429429b7a2
%%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 2012-03-01 12:00:00 ... 2012-03-31 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 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> mask2d (y, x) bool 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) 2022-08-04 13:00:42,876 - distributed.worker - ERROR - Worker stream died during communication: tcp://127.0.0.1:45340 Traceback (most recent call last): File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/site-packages/distributed/comm/tcp.py", line 223, in read frames_nbytes = await stream.read_bytes(fmt_size) 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 456, 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 328, in connect handshake = await asyncio.wait_for(comm.read(), time_left()) File "/ccc/cont003/home/ra5563/ra5563/monitor/lib/python3.10/asyncio/tasks.py", line 458, 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://127.0.0.1:45340 after 30 s 2022-08-04 13:01:03,111 - distributed.worker - ERROR - Worker stream died during communication: tcp://127.0.0.1:45340 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://127.0.0.1:45340 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) 2022-08-04 13:01:03,620 - distributed.worker - ERROR - Worker stream died during communication: tcp://127.0.0.1:45340 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://127.0.0.1:45340 after 30 s 2022-08-04 13:01:03,841 - distributed.worker - ERROR - Worker stream died during communication: tcp://127.0.0.1:45340 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://127.0.0.1:45340 after 30 s 2022-08-04 13:01:03,888 - distributed.worker - ERROR - Worker stream died during communication: tcp://127.0.0.1:45340 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://127.0.0.1:45340 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)
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)
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)
slice(3, 4, None) slice(4, 5, None) 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) slice(15, 16, None) slice(16, 17, None)
2022-08-04 13:11:01,395 - distributed.utils_perf - WARNING - full garbage collections took 10% CPU time recently (threshold: 10%)
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slice(18, 19, None) slice(19, 20, None)
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slice(20, 21, None)
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slice(21, 22, None)
2022-08-04 13:13:49,884 - distributed.utils_perf - WARNING - full garbage collections took 10% CPU time recently (threshold: 10%) 2022-08-04 13:13:52,463 - distributed.utils_perf - WARNING - full garbage collections took 10% CPU time recently (threshold: 10%)
slice(22, 23, None)
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slice(23, 24, None)
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slice(25, 26, None)
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slice(26, 27, None)
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slice(27, 28, None)
2022-08-04 13:17:02,433 - distributed.utils_perf - WARNING - full garbage collections took 10% CPU time recently (threshold: 10%) 2022-08-04 13:17:05,516 - distributed.utils_perf - WARNING - full garbage collections took 10% CPU time recently (threshold: 10%) 2022-08-04 13:17:07,046 - distributed.utils_perf - WARNING - full garbage collections took 10% CPU time recently (threshold: 10%)
slice(28, 29, None)
2022-08-04 13:17:35,619 - distributed.utils_perf - WARNING - full garbage collections took 10% CPU time recently (threshold: 10%) 2022-08-04 13:17:39,487 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 13:17:43,230 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%)
slice(29, 30, None)
2022-08-04 13:18:07,927 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 13:18:10,786 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%) 2022-08-04 13:18:32,270 - distributed.utils_perf - WARNING - full garbage collections took 11% CPU time recently (threshold: 10%)
slice(30, 31, None)
2022-08-04 13:18:41,403 - distributed.utils_perf - WARNING - full garbage collections took 12% CPU time recently (threshold: 10%) 2022-08-04 13:18:43,822 - distributed.utils_perf - WARNING - full garbage collections took 12% CPU time recently (threshold: 10%)
CPU times: user 10min 59s, sys: 1min 31s, total: 12min 30s Wall time: 19min 13s