Closed scottyhq closed 5 years ago
@scottyhq Do you have access to the server logs? Do they have any interesting information in them?
I'd still be wary about tornado 6...
we've pinned to tornado 5.1.1. I see the following message in the log: [W 2019-05-21 23:04:04.105 SingleUserLabApp handlers:620] object KubeCluster can't be used in 'await' expression
Hmm, I'm not sure. @mrocklin does this look familiar? I wonder if it's a regression in dask-kubernetes
.
Actually... i'm suspicious this is something to do with the a new version of repo2docker and some mixing of environments (https://github.com/pangeo-data/pangeo-stacks/issues/47). Because if I list the packages in the 'base' environment we have the following (including tornado 6.0.2):
(base) jovyan@~:conda list
# packages in environment at /srv/conda:
#
# Name Version Build Channel
absl-py 0.7.1 py36_0 conda-forge
affine 2.2.2 py_0 conda-forge
antlr-python-runtime 4.7.2 py36_1000 conda-forge
appdirs 1.4.3 py_1 conda-forge
asciitree 0.3.3 py_2 conda-forge
asn1crypto 0.24.0 py36_1003 conda-forge
astor 0.7.1 py_0 conda-forge
attrdict 2.0.1 py_0 conda-forge
attrs 19.1.0 py_0 conda-forge
backcall 0.1.0 py_0 conda-forge
beautifulsoup4 4.7.1 py36_1001 conda-forge
bleach 3.1.0 py_0 conda-forge
blinker 1.4 py_1 conda-forge
blosc 1.16.3 hf484d3e_0 conda-forge
bokeh 1.1.0 py36_0 conda-forge
boost-cpp 1.68.0 h11c811c_1000 conda-forge
boto3 1.9.151 py_0 conda-forge
botocore 1.12.151 py_0 conda-forge
branca 0.3.1 py_0 conda-forge
bzip2 1.0.6 h14c3975_1002 conda-forge
c-ares 1.15.0 h14c3975_1001 conda-forge
ca-certificates 2019.3.9 hecc5488_0 conda-forge
cachetools 2.1.0 py_0 conda-forge
cairo 1.16.0 ha4e643d_1000 conda-forge
cartopy 0.17.0 py36h0aa2c8f_1004 conda-forge
certifi 2019.3.9 py36_0 conda-forge
cf-units 2.1.1 py36h3010b51_1000 conda-forge
cffi 1.12.3 py36h8022711_0 conda-forge
cftime 1.0.3.4 py36hd352d35_1001 conda-forge
chardet 3.0.4 py36_1003 conda-forge
click 7.0 py_0 conda-forge
click-plugins 1.1.1 py_0 conda-forge
cligj 0.5.0 py_0 conda-forge
climlab 0.7.3 py36h4c70da7_0 conda-forge
cloudpickle 1.0.0 py_0 conda-forge
colorcet 2.0.1 py_0 conda-forge
conda 4.6.14 py36_0 conda-forge
configobj 5.0.6 py_0 conda-forge
cryptography 2.6.1 py36h72c5cf5_0 conda-forge
curl 7.64.1 hf8cf82a_0 conda-forge
cycler 0.10.0 py_1 conda-forge
cytoolz 0.9.0.1 py36h14c3975_1001 conda-forge
dask 1.2.2 py_0 conda-forge
dask-core 1.2.2 py_0 conda-forge
dask-glm 0.1.0 0 conda-forge
dask-ml 0.12.0 py_0 conda-forge
datashader 0.7.0 py_0 conda-forge
datashape 0.5.4 py_1 conda-forge
dbus 1.13.6 he372182_0 conda-forge
decorator 4.4.0 py_0 conda-forge
defusedxml 0.5.0 py_1 conda-forge
descartes 1.1.0 py_3 conda-forge
distributed 1.28.1 py36_0 conda-forge
docopt 0.6.2 py_1 conda-forge
docrep 0.2.5 py_0 conda-forge
docutils 0.14 py36_1001 conda-forge
entrypoints 0.3 py36_1000 conda-forge
eofs 1.4.0 py_0 conda-forge
esmf 7.1.0 hdfb41a0_1004 conda-forge
esmpy 7.1.0 py36h24bf2e0_3 conda-forge
expat 2.2.5 hf484d3e_1002 conda-forge
fasteners 0.14.1 py_3 conda-forge
fiona 1.8.6 py36hf242f0b_3 conda-forge
fontconfig 2.13.1 he4413a7_1000 conda-forge
freetype 2.10.0 he983fc9_0 conda-forge
freexl 1.0.5 h14c3975_1002 conda-forge
future 0.17.1 py36_1000 conda-forge
gast 0.2.2 py_0 conda-forge
gcsfs 0.2.2 py_0 conda-forge
gdal 2.4.1 py36hf242f0b_0 conda-forge
geopandas 0.5.0 py_2 conda-forge
geos 3.7.1 hf484d3e_1000 conda-forge
geotiff 1.4.3 h1105359_1000 conda-forge
geoviews 1.6.2 py_0 conda-forge
geoviews-core 1.6.2 py_0 conda-forge
gettext 0.19.8.1 hc5be6a0_1002 conda-forge
giflib 5.1.7 h516909a_1 conda-forge
glib 2.58.3 hf63aee3_1001 conda-forge
google-auth 1.6.3 py_0 conda-forge
google-auth-oauthlib 0.3.0 py_0 conda-forge
grpcio 1.16.1 py36hf8bcb03_1 defaults
gst-plugins-base 1.14.4 hdf3bae2_1001 conda-forge
gstreamer 1.14.4 h66beb1c_1001 conda-forge
gsw 3.3.1 py36h516909a_0 conda-forge
h5netcdf 0.7.1 py_0 conda-forge
h5py 2.9.0 nompi_py36hf008753_1102 conda-forge
hdf4 4.2.13 h9a582f1_1002 conda-forge
hdf5 1.10.4 nompi_h3c11f04_1106 conda-forge
heapdict 1.0.0 py36_1000 conda-forge
holoviews 1.12.2 py_0 conda-forge
hvplot 0.4.0 py_1 conda-forge
icu 58.2 hf484d3e_1000 conda-forge
idna 2.8 py36_1000 conda-forge
imageio 2.5.0 py36_0 conda-forge
intake 0.5.0 py_0 conda-forge
intake-esm 2019.5.11 py_0 conda-forge
intake-xarray 0.3.0 py_0 conda-forge
ipykernel 5.1.1 py36h24bf2e0_0 conda-forge
ipyleaflet 0.10.2 py36_0 conda-forge
ipython 7.5.0 py36h24bf2e0_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.4.2 py_0 conda-forge
iris 2.2.0 py36_1003 conda-forge
jedi 0.13.3 py36_0 conda-forge
jinja2 2.10.1 py_0 conda-forge
jmespath 0.9.4 py_0 conda-forge
joblib 0.13.2 py_0 conda-forge
jpeg 9c h14c3975_1001 conda-forge
json-c 0.13.1 h14c3975_1001 conda-forge
jsonschema 3.0.1 py36_0 conda-forge
jupyter 1.0.0 py_2 conda-forge
jupyter_client 5.2.4 py_3 conda-forge
jupyter_console 6.0.0 py_0 conda-forge
jupyter_core 4.4.0 py_0 conda-forge
kealib 1.4.10 h1978553_1003 conda-forge
keras 2.2.4 py36_1 conda-forge
keras-applications 1.0.7 py_1 conda-forge
keras-preprocessing 1.0.9 py_1 conda-forge
kiwisolver 1.1.0 py36hc9558a2_0 conda-forge
krb5 1.16.3 h05b26f9_1001 conda-forge
libblas 3.8.0 10_openblas conda-forge
libcblas 3.8.0 10_openblas conda-forge
libcurl 7.64.1 hda55be3_0 conda-forge
libdap4 3.19.1 hd48c02d_1000 conda-forge
libedit 3.1.20181209 hc058e9b_0 defaults
libffi 3.2.1 hd88cf55_4 defaults
libgcc-ng 8.2.0 hdf63c60_1 defaults
libgdal 2.4.1 hdb8f723_0 conda-forge
libgfortran-ng 7.3.0 hdf63c60_0 defaults
libgpuarray 0.7.6 h14c3975_1003 conda-forge
libiconv 1.15 h516909a_1005 conda-forge
libkml 1.3.0 h328b03d_1009 conda-forge
liblapack 3.8.0 10_openblas conda-forge
libnetcdf 4.6.2 hbdf4f91_1001 conda-forge
libpng 1.6.37 hed695b0_0 conda-forge
libpq 11.3 h4e4e079_0 conda-forge
libprotobuf 3.7.1 h8b12597_0 conda-forge
libsodium 1.0.16 h14c3975_1001 conda-forge
libspatialindex 1.9.0 he1b5a44_0 conda-forge
libspatialite 4.3.0a hb5ec416_1026 conda-forge
libssh2 1.8.2 h22169c7_2 conda-forge
libstdcxx-ng 8.2.0 hdf63c60_1 defaults
libtiff 4.0.10 h648cc4a_1001 conda-forge
libuuid 2.32.1 h14c3975_1000 conda-forge
libxcb 1.13 h14c3975_1002 conda-forge
libxml2 2.9.9 h13577e0_0 conda-forge
libxslt 1.1.32 h4785a14_1002 conda-forge
llvmlite 0.28.0 py36hdbcaa40_0 conda-forge
locket 0.2.0 py_2 conda-forge
lxml 4.3.3 py36h7ec2d77_0 conda-forge
lz4 2.1.6 py36hd79334b_1001 conda-forge
lz4-c 1.8.3 he1b5a44_1001 conda-forge
mako 1.0.7 py_1 conda-forge
mapclassify 2.0.1 py_0 conda-forge
markdown 2.6.11 py_0 conda-forge
markupsafe 1.1.1 py36h14c3975_0 conda-forge
matplotlib 3.0.3 py36_1 conda-forge
matplotlib-base 3.0.3 py36h5f35d83_1 conda-forge
mechanicalsoup 0.11.0 py_0 conda-forge
mercantile 1.0.4 pypi_0 pypi
metpy 0.10.0 py36_1001 conda-forge
mistune 0.8.4 py36h14c3975_1000 conda-forge
mock 3.0.5 py36_0 conda-forge
monotonic 1.5 py_0 conda-forge
mpi 1.0 mpich conda-forge
mpich 3.2.1 h1c2f66e_1008 conda-forge
msgpack-numpy 0.4.4.3 py_0 conda-forge
msgpack-python 0.6.1 py36h6bb024c_0 conda-forge
multipledispatch 0.6.0 py_0 conda-forge
munch 2.3.2 py_0 conda-forge
nbconvert 5.5.0 py_0 conda-forge
nbformat 4.4.0 py_1 conda-forge
ncurses 6.1 he6710b0_1 defaults
netcdf-fortran 4.4.5 hea25ff8_1000 conda-forge
netcdf4 1.5.1.2 py36had58050_0 conda-forge
networkx 2.3 py_0 conda-forge
ninja 1.9.0 h6bb024c_0 conda-forge
notebook 5.7.8 py36_0 conda-forge
numba 0.43.1 py36hf2d7682_0 conda-forge
numcodecs 0.6.3 py36hf484d3e_0 conda-forge
numpy 1.16.3 py36he5ce36f_0 conda-forge
oauthlib 3.0.1 py_0 conda-forge
olefile 0.46 py_0 conda-forge
openblas 0.3.6 h6e990d7_2 conda-forge
openjpeg 2.3.1 h58a6597_0 conda-forge
openssl 1.1.1b h14c3975_1 conda-forge
owslib 0.17.1 py_0 conda-forge
packaging 19.0 py_0 conda-forge
pandas 0.24.2 py36hf484d3e_0 conda-forge
pandoc 2.7.2 0 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
panel 0.5.1 h24bf2e0_2 conda-forge
param 1.9.0 py_0 conda-forge
parso 0.4.0 py_0 conda-forge
partd 0.3.9 py_0 conda-forge
pcre 8.41 hf484d3e_1003 conda-forge
pexpect 4.7.0 py36_0 conda-forge
pickleshare 0.7.5 py36_1000 conda-forge
pillow 6.0.0 py36he7afcd5_0 conda-forge
pint 0.9 py36_2 conda-forge
pip 19.1 py36_0 conda-forge
pixman 0.34.0 h14c3975_1003 conda-forge
pooch 0.2.1 py36_1000 conda-forge
poppler 0.67.0 h2ad7f00_6 conda-forge
poppler-data 0.4.9 1 conda-forge
postgresql 11.3 hbeee2d4_0 conda-forge
proj4 5.2.0 h14c3975_1001 conda-forge
prometheus_client 0.6.0 py_0 conda-forge
prompt_toolkit 2.0.9 py_0 conda-forge
protobuf 3.7.1 py36he1b5a44_0 conda-forge
psutil 5.6.2 py36h516909a_0 conda-forge
pthread-stubs 0.4 h14c3975_1001 conda-forge
ptyprocess 0.6.0 py_1001 conda-forge
pyasn1 0.4.4 py_1 conda-forge
pyasn1-modules 0.2.4 py_0 conda-forge
pycosat 0.6.3 py36h14c3975_1001 conda-forge
pycparser 2.19 py36_1 conda-forge
pyct 0.4.6 py_0 conda-forge
pyct-core 0.4.6 py_0 conda-forge
pydap 3.2.2 py36_1000 conda-forge
pyepsg 0.4.0 py_0 conda-forge
pygments 2.4.0 py_0 conda-forge
pygpu 0.7.6 py36h3010b51_1000 conda-forge
pyjwt 1.7.1 py_0 conda-forge
pykdtree 1.3.1 py36h3010b51_1002 conda-forge
pyke 1.1.1 py36_1000 conda-forge
pyopenssl 19.0.0 py36_0 conda-forge
pyorbital 1.5.0 py_0 conda-forge
pyparsing 2.4.0 py_0 conda-forge
pyproj 1.9.6 py36hc0953d3_1000 conda-forge
pyqt 5.9.2 py36hcca6a23_0 conda-forge
pyresample 1.12.3 py36hf2d7682_0 conda-forge
pyrsistent 0.15.2 py36h516909a_0 conda-forge
pyshp 2.1.0 py_0 conda-forge
pysocks 1.7.0 py36_0 conda-forge
pyspectral 0.8.8 py_0 conda-forge
pyspharm 1.0.9 py36h6091dcd_1003 conda-forge
python 3.6.7 h381d211_1004 conda-forge
python-blosc 1.8.1 py36hf484d3e_0 conda-forge
python-dateutil 2.8.0 py_0 conda-forge
python-geotiepoints 1.1.8 py36hd352d35_0 conda-forge
python-snappy 0.5.4 py36hee44bf9_0 conda-forge
pytorch-cpu 1.0.1 py36hf484d3e_0 conda-forge
pytz 2019.1 py_0 conda-forge
pyviz_comms 0.7.2 py_0 conda-forge
pywavelets 1.0.3 py36hd352d35_1 conda-forge
pyyaml 5.1 py36h14c3975_0 conda-forge
pyzmq 18.0.1 py36hc4ba49a_1 conda-forge
qt 5.9.7 h52cfd70_1 conda-forge
qtconsole 4.4.4 py_0 conda-forge
rasterio 1.0.23 py36h5b3f9e8_0 conda-forge
readline 7.0 h7b6447c_5 defaults
regionmask 0.4.0 pypi_0 pypi
requests 2.22.0 py36_0 conda-forge
requests-oauthlib 1.2.0 py_0 conda-forge
rio-cogeo 1.0.0 pypi_0 pypi
rsa 3.4.2 py_1 conda-forge
rtree 0.8.3 py36h666c49c_1002 conda-forge
ruamel 1.0 py36_0 conda-forge
ruamel.yaml 0.15.96 py36h516909a_0 conda-forge
ruamel_yaml 0.15.71 py36h14c3975_1000 conda-forge
s3fs 0.2.1 py_0 conda-forge
s3transfer 0.2.0 py36_0 conda-forge
satpy 0.15.1 pyh326bf55_0 conda-forge
scikit-image 0.15.0 py36he1b5a44_0 conda-forge
scikit-learn 0.21.1 py36h627018c_0 conda-forge
scipy 1.2.1 py36h09a28d5_1 conda-forge
send2trash 1.5.0 py_0 conda-forge
setuptools 41.0.1 py36_0 conda-forge
shapely 1.6.4 py36h2afed24_1004 conda-forge
sip 4.19.8 py36hf484d3e_1000 conda-forge
six 1.12.0 py36_1000 conda-forge
snappy 1.1.7 hf484d3e_1002 conda-forge
snuggs 1.4.6 py_0 conda-forge
sortedcontainers 2.1.0 py_0 conda-forge
soupsieve 1.9.1 py36_0 conda-forge
sqlite 3.27.2 h7b6447c_0 defaults
supermercado 0.0.5 pypi_0 pypi
tblib 1.3.2 py_1 conda-forge
tensorboard 1.13.1 py36_0 conda-forge
tensorflow 1.13.1 py36_0 conda-forge
tensorflow-estimator 1.13.0 py_0 defaults
termcolor 1.1.0 py_2 conda-forge
terminado 0.8.2 py36_0 conda-forge
testpath 0.3.1 py36_1 conda-forge
theano 1.0.3 py36_0 conda-forge
tk 8.6.9 h84994c4_1001 conda-forge
toolz 0.9.0 py_1 conda-forge
tornado 6.0.2 py36h516909a_0 conda-forge
tqdm 4.32.1 py_0 conda-forge
traitlets 4.3.2 py36_1000 conda-forge
traittypes 0.2.1 py_1 conda-forge
trollimage 1.8.0 py_0 conda-forge
trollsift 0.3.2 py_0 conda-forge
tzcode 2018g h14c3975_1001 conda-forge
udunits2 2.2.27.6 h4e0c4b3_1001 conda-forge
urllib3 1.24.3 py36_0 conda-forge
wcwidth 0.1.7 py_1 conda-forge
webencodings 0.5.1 py_1 conda-forge
webob 1.8.5 py_0 conda-forge
werkzeug 0.15.4 py_0 conda-forge
wheel 0.33.4 py36_0 conda-forge
widgetsnbextension 3.4.2 py36_1000 conda-forge
windspharm 1.7.0 py36_1000 conda-forge
xarray 0.12.1 py_0 conda-forge
xerces-c 3.2.2 hac72e42_1001 conda-forge
xesmf 0.1.1 py36_1 conda-forge
xgcm 0.2.0 py_0 conda-forge
xorg-kbproto 1.0.7 h14c3975_1002 conda-forge
xorg-libice 1.0.9 h516909a_1004 conda-forge
xorg-libsm 1.2.3 h84519dc_1000 conda-forge
xorg-libx11 1.6.7 h14c3975_1000 conda-forge
xorg-libxau 1.0.9 h14c3975_0 conda-forge
xorg-libxdmcp 1.1.3 h516909a_0 conda-forge
xorg-libxext 1.3.4 h516909a_0 conda-forge
xorg-libxrender 0.9.10 h516909a_1002 conda-forge
xorg-renderproto 0.11.1 h14c3975_1002 conda-forge
xorg-xextproto 7.3.0 h14c3975_1002 conda-forge
xorg-xproto 7.0.31 h14c3975_1007 conda-forge
xrft 0.2.0 py_0 conda-forge
xz 5.2.4 h14c3975_4 defaults
yaml 0.1.7 had09818_2 defaults
zarr 2.3.1 py36_0 conda-forge
zeromq 4.3.1 hf484d3e_1000 conda-forge
zict 0.1.4 py_0 conda-forge
zlib 1.2.11 h7b6447c_3 defaults
My first guess would be JupyterLab + Tornado 6 conflicts. I don't think that dask-kubernetes has changed a ton recently, but @jhamman might know more.
dask-kubernetes
had a release four days ago. Worth checking, I think.
Fair point
@ian-r-rose - given multiple conda environments on a jupyterhub, which does dask labextension use by default?
Whichever one is used to launch JupyterLab, I think.
@scottyhq - can you try with a LocalCluster and see if that works? That will help determine if its in KubeCluster or not.
Just to clarify, launching a KubeCluster programmatically works, and I can use the 'search' glass to find it and activate all buttons. It is the 'clusters +new' part that is non-responsive. If anyone wants to enter the hub and explore further, see the hub link in the first comment.
import dask
from dask_kubernetes import KubeCluster
from dask.distributed import Client
from dask.distributed import wait, progress
cluster = KubeCluster(n_workers=2)
cluster
Oh, yeah, launching clusters through the lab extension requires that they support async/await. This is the whole reason for the async development branch in dask kubernetes.
On Tue, May 21, 2019, 6:42 PM Scott Henderson notifications@github.com wrote:
Just to clarify, launching a KubeCluster programmatically works, and I can use the 'search' glass to find it and activate all buttons. It is the 'clusters +new' part that is non-responsive. If anyone wants to enter the hub and explore further, see the hub link in the first comment.
import daskfrom dask_kubernetes import KubeClusterfrom dask.distributed import Clientfrom dask.distributed import wait, progress cluster = KubeCluster(n_workers=2) cluster
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Has that not been merged/published yet?
Has that not been merged/published yet?
No, its still sitting in the dev
brach.
This binder does a few things:
dev
branch of dask_kubernetesFull specs here: https://github.com/jhamman/pangeo_test_binder/tree/dask_dev
Is there anything that should be done to move forwards with an async-aware dask-kubernetes
? I hadn't realized we were still blocking on that.
There are a couple things to do, yes. Mostly it needs to be used and bugs need to be found and fixed. I plan to write up the state of things and a few possible plans as an issue later this week.
@mrocklin I should have time to push on async KubeCluster (not this week, but probably next week). Is that something you'd like me to take on?
That would be very welcome. @quasiben has some work. Also, I can also imagine a future in which we make a Worker-like class that manages a Pod, and then just use SpecCluster around that class. I'd be happy to have a chat any time about options here if you're interested.
On Tue, Jun 4, 2019 at 1:56 PM Tom Augspurger notifications@github.com wrote:
@mrocklin https://github.com/mrocklin I should have time to push on async KubeCluster (not this week, but probably next week). Is that something you'd like me to take on?
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If it will take a significant amount of time, we can also back out the changes that make dask-labextension
expect an asynchronously started cluster.
@TomAugspurger there are two PRs for async kube if you are interested:
I would suggest looking at @mrocklin 's before mine.
noting that once upcoming async changes to dask-kubernetes are merged and released we should bump to dask-labextension > 1.0
The most recent images did away with pinning most versions: https://github.com/pangeo-data/pangeo-stacks/issues/42
Unfortunately in running these new images, the dask labextension is no longer able to launch new KubeClusters (you can select the latest image to run on this hub: https://nasa.pangeo.io)
Seeing messages such as these:
And here is a copy of the full conda environment installed:
pinging @ian-r-rose @jhamman