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Empty output (sometimes) for dask=2022.12.1 #1206

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jbednar opened this issue Apr 28, 2023 · 5 comments
Closed

Empty output (sometimes) for dask=2022.12.1 #1206

jbednar opened this issue Apr 28, 2023 · 5 comments
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@ianthomas23

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@jbednar
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jbednar commented Apr 28, 2023 •
edited
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For this code:

import datashader as ds, dask, dask.dataframe as dd

df = dd.read_parquet('./data/census2010.parq', engine='fastparquet')
df = df.persist()

cvs = ds.Canvas(plot_width=900, plot_height=525)
agg = cvs.points(df, 'easting', 'northing')

ds.tf.shade(agg, how='eq_hist')

import holoviews as hv
from holoviews.operation.datashader import datashade, dynspread
hv.extension('bokeh')

points = hv.Points(hv.Dataset(df, kdims=['easting', 'northing']))
datashade(points).opts(width=930, height=525)

the usual output is:

image

With dask=2022.11.1 or earlier, the HoloViews plot can be zoomed at will, and rerenders reliably. However, with dask=2022.12.1 (or later, up to the current version 2023.4.0), sometimes there is no output rendered for ds.tf.shade(agg, how='eq_hist'), and zooming in and out of the HoloViews plot soon gives various errors that suggest an empty output as well:

  File "/Users/jbednar/examples/census/envs/default/lib/python3.10/asyncio/events.py", line 80, in _run
    self._context.run(self._callback, *self._args)
  File "/Users/jbednar/examples/census/envs/default/lib/python3.10/site-packages/tornado/platform/asyncio.py", line 192, in _handle_events
    handler_func(fileobj, events)
  File "/Users/jbednar/examples/census/envs/default/lib/python3.10/site-packages/tornado/iostream.py", line 695, in _handle_events
    self._handle_write()
  File "/Users/jbednar/examples/census/envs/default/lib/python3.10/site-packages/tornado/iostream.py", line 965, in _handle_write
    self._write_buffer.advance(num_bytes)
  File "/Users/jbednar/examples/census/envs/default/lib/python3.10/site-packages/tornado/iostream.py", line 182, in advance
    assert 0 < size <= self._size
AssertionError

After those errors start, the plot no longer re-renders.
@jbednar
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jbednar commented Apr 28, 2023

I created the dask=2022.11.1 (working) environment censusold with the command:

conda create -y -n censusold -c conda-forge python=3.9 notebook dask=2022.11.1 datashader fastparquet python-snappy 'pandas<2' holoviews

# packages in environment at /Users/jbednar/miniconda3/envs/censusold:
#
# Name                    Version                   Build  Channel
anyio                     3.6.2              pyhd8ed1ab_0    conda-forge
appnope                   0.1.3              pyhd8ed1ab_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0           py39ha30fb19_3    conda-forge
asttokens                 2.2.1              pyhd8ed1ab_0    conda-forge
attrs                     22.2.0             pyh71513ae_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.2             pyha770c72_0    conda-forge
bleach                    6.0.0              pyhd8ed1ab_0    conda-forge
bokeh                     2.4.3              pyhd8ed1ab_3    conda-forge
brotli                    1.0.9                hb7f2c08_8    conda-forge
brotli-bin                1.0.9                hb7f2c08_8    conda-forge
brotlipy                  0.7.0           py39ha30fb19_1005    conda-forge
bzip2                     1.0.8                h0d85af4_4    conda-forge
ca-certificates           2022.12.7            h033912b_0    conda-forge
certifi                   2022.12.7          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1           py39h131948b_3    conda-forge
charset-normalizer        3.1.0              pyhd8ed1ab_0    conda-forge
click                     8.1.3           unix_pyhd8ed1ab_2    conda-forge
cloudpickle               2.2.1              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
colorcet                  3.0.1              pyhd8ed1ab_0    conda-forge
comm                      0.1.3              pyhd8ed1ab_0    conda-forge
contourpy                 1.0.7            py39h92daf61_0    conda-forge
cramjam                   2.6.2            py39hd4bc93a_0    conda-forge
cryptography              40.0.2           py39hbeae22c_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cytoolz                   0.12.0           py39ha30fb19_1    conda-forge
dask                      2022.11.1          pyhd8ed1ab_0    conda-forge
dask-core                 2022.11.1          pyhd8ed1ab_0    conda-forge
datashader                0.14.4             pyh1a96a4e_0    conda-forge
datashape                 0.5.4                      py_1    conda-forge
debugpy                   1.6.7            py39h7a8716b_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
distributed               2022.11.1          pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
fastparquet               2023.2.0         py39h7cc1f47_0    conda-forge
flit-core                 3.8.0              pyhd8ed1ab_0    conda-forge
fonttools                 4.39.3           py39ha30fb19_0    conda-forge
freetype                  2.12.1               h3f81eb7_1    conda-forge
fsspec                    2023.4.0           pyh1a96a4e_0    conda-forge
holoviews                 1.15.4             pyhd8ed1ab_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
importlib-metadata        6.6.0              pyha770c72_0    conda-forge
importlib-resources       5.12.0             pyhd8ed1ab_0    conda-forge
importlib_resources       5.12.0             pyhd8ed1ab_0    conda-forge
ipykernel                 6.22.0             pyh736e0ef_0    conda-forge
ipython                   8.12.0             pyhd1c38e8_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
jedi                      0.18.2             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge
jupyter_client            7.3.4              pyhd8ed1ab_0    conda-forge
jupyter_core              5.3.0            py39h6e9494a_0    conda-forge
jupyter_server            1.23.6             pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
kiwisolver                1.4.4            py39h92daf61_1    conda-forge
lcms2                     2.15                 h2dcdeff_1    conda-forge
lerc                      4.0.0                hb486fe8_0    conda-forge
libblas                   3.9.0           16_osx64_openblas    conda-forge
libbrotlicommon           1.0.9                hb7f2c08_8    conda-forge
libbrotlidec              1.0.9                hb7f2c08_8    conda-forge
libbrotlienc              1.0.9                hb7f2c08_8    conda-forge
libcblas                  3.9.0           16_osx64_openblas    conda-forge
libcxx                    16.0.2               hd57cbcb_0    conda-forge
libdeflate                1.18                 hac1461d_0    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libgfortran               5.0.0           11_3_0_h97931a8_31    conda-forge
libgfortran5              12.2.0              he409387_31    conda-forge
libjpeg-turbo             2.1.5.1              hb7f2c08_0    conda-forge
liblapack                 3.9.0           16_osx64_openblas    conda-forge
libllvm11                 11.1.0               h8fb7429_5    conda-forge
libopenblas               0.3.21          openmp_h429af6e_3    conda-forge
libpng                    1.6.39               ha978bb4_0    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
libsqlite                 3.40.0               ha978bb4_1    conda-forge
libtiff                   4.5.0                hedf67fa_6    conda-forge
libwebp-base              1.3.0                hb7f2c08_0    conda-forge
libxcb                    1.13              h0d85af4_1004    conda-forge
libzlib                   1.2.13               hfd90126_4    conda-forge
llvm-openmp               16.0.2               hff08bdf_0    conda-forge
llvmlite                  0.39.1           py39had167e2_1    conda-forge
locket                    1.0.0              pyhd8ed1ab_0    conda-forge
lz4                       4.3.2            py39hd0af75a_0    conda-forge
lz4-c                     1.9.4                hf0c8a7f_0    conda-forge
markdown                  3.4.3              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.2            py39ha30fb19_0    conda-forge
matplotlib-base           3.7.1            py39hb2f573b_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mistune                   2.0.5              pyhd8ed1ab_0    conda-forge
msgpack-python            1.0.5            py39h92daf61_0    conda-forge
multipledispatch          0.6.0                      py_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nbclassic                 0.5.6              pyh8b2e9e2_0    conda-forge
nbclient                  0.7.4              pyhd8ed1ab_0    conda-forge
nbconvert-core            7.3.1              pyhd8ed1ab_0    conda-forge
nbformat                  5.8.0              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h96cf925_1    conda-forge
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
notebook                  6.5.4              pyha770c72_0    conda-forge
notebook-shim             0.2.3              pyhd8ed1ab_0    conda-forge
numba                     0.56.4           py39h6e2ba77_1    conda-forge
numpy                     1.23.5           py39hdfa1d0c_0    conda-forge
openjpeg                  2.5.0                h13ac156_2    conda-forge
openssl                   3.1.0                h8a1eda9_2    conda-forge
packaging                 23.1               pyhd8ed1ab_0    conda-forge
pandas                    1.5.3            py39hecff1ad_1    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
panel                     0.14.4             pyhd8ed1ab_0    conda-forge
param                     1.13.0             pyh1a96a4e_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
partd                     1.4.0              pyhd8ed1ab_0    conda-forge
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.5.0            py39h77c96bc_0    conda-forge
pip                       23.1.2             pyhd8ed1ab_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
platformdirs              3.5.0              pyhd8ed1ab_0    conda-forge
pooch                     1.7.0              pyha770c72_3    conda-forge
prometheus_client         0.16.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.38             pyha770c72_0    conda-forge
prompt_toolkit            3.0.38               hd8ed1ab_0    conda-forge
psutil                    5.9.5            py39ha30fb19_0    conda-forge
pthread-stubs             0.4               hc929b4f_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pyct                      0.4.6                      py_0    conda-forge
pyct-core                 0.4.6                      py_0    conda-forge
pygments                  2.15.1             pyhd8ed1ab_0    conda-forge
pyobjc-core               9.1.1            py39h0504f80_0    conda-forge
pyobjc-framework-cocoa    9.1.1            py39h0504f80_0    conda-forge
pyopenssl                 23.1.1             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyrsistent                0.19.3           py39ha30fb19_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.9.16          h709bd14_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.16.3             pyhd8ed1ab_0    conda-forge
python-snappy             0.6.1            py39hf74c2c1_0    conda-forge
python_abi                3.9                      3_cp39    conda-forge
pytz                      2023.3             pyhd8ed1ab_0    conda-forge
pyviz_comms               2.2.1              pyhd8ed1ab_1    conda-forge
pyyaml                    6.0              py39ha30fb19_5    conda-forge
pyzmq                     25.0.2           py39hed8f129_0    conda-forge
readline                  8.2                  h9e318b2_1    conda-forge
requests                  2.29.0             pyhd8ed1ab_0    conda-forge
scipy                     1.10.1           py39h4c5e66d_0    conda-forge
send2trash                1.8.2              pyhd1c38e8_0    conda-forge
setuptools                67.7.2             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
snappy                    1.1.10               h225ccf5_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
sortedcontainers          2.4.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.3.2.post1        pyhd8ed1ab_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
tblib                     1.7.0              pyhd8ed1ab_0    conda-forge
terminado                 0.17.1             pyhd1c38e8_0    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h5dbffcc_0    conda-forge
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
tornado                   6.1              py39h63b48b0_3    conda-forge
tqdm                      4.65.0             pyhd8ed1ab_1    conda-forge
traitlets                 5.9.0              pyhd8ed1ab_0    conda-forge
typing-extensions         4.5.0                hd8ed1ab_0    conda-forge
typing_extensions         4.5.0              pyha770c72_0    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
unicodedata2              15.0.0           py39ha30fb19_0    conda-forge
urllib3                   1.26.15            pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.6              pyhd8ed1ab_0    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.5.1              pyhd8ed1ab_0    conda-forge
wheel                     0.40.0             pyhd8ed1ab_0    conda-forge
xarray                    2023.4.2           pyhd8ed1ab_0    conda-forge
xorg-libxau               1.0.9                h35c211d_0    conda-forge
xorg-libxdmcp             1.1.3                h35c211d_0    conda-forge
xz                        5.2.6                h775f41a_0    conda-forge
yaml                      0.2.5                h0d85af4_2    conda-forge
zeromq                    4.3.4                he49afe7_1    conda-forge
zict                      3.0.0              pyhd8ed1ab_0    conda-forge
zipp                      3.15.0             pyhd8ed1ab_0    conda-forge
zstd                      1.5.2                hbc0c0cd_6    conda-forge

@jbednar
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jbednar commented Apr 28, 2023

I created the dask=2022.12.1 (not working) environment censusnew with the command:

conda create -y -n censusnew -c conda-forge python=3.9 notebook dask=2022.12.1 datashader fastparquet python-snappy 'pandas<2' holoviews

# packages in environment at /Users/jbednar/miniconda3/envs/censusnew:
#
# Name                    Version                   Build  Channel
anyio                     3.6.2              pyhd8ed1ab_0    conda-forge
appnope                   0.1.3              pyhd8ed1ab_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0           py39ha30fb19_3    conda-forge
asttokens                 2.2.1              pyhd8ed1ab_0    conda-forge
attrs                     22.2.0             pyh71513ae_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.2             pyha770c72_0    conda-forge
bleach                    6.0.0              pyhd8ed1ab_0    conda-forge
bokeh                     2.4.3              pyhd8ed1ab_3    conda-forge
brotli                    1.0.9                hb7f2c08_8    conda-forge
brotli-bin                1.0.9                hb7f2c08_8    conda-forge
brotlipy                  0.7.0           py39ha30fb19_1005    conda-forge
bzip2                     1.0.8                h0d85af4_4    conda-forge
ca-certificates           2022.12.7            h033912b_0    conda-forge
certifi                   2022.12.7          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1           py39h131948b_3    conda-forge
charset-normalizer        3.1.0              pyhd8ed1ab_0    conda-forge
click                     8.1.3           unix_pyhd8ed1ab_2    conda-forge
cloudpickle               2.2.1              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
colorcet                  3.0.1              pyhd8ed1ab_0    conda-forge
comm                      0.1.3              pyhd8ed1ab_0    conda-forge
contourpy                 1.0.7            py39h92daf61_0    conda-forge
cramjam                   2.6.2            py39hd4bc93a_0    conda-forge
cryptography              40.0.2           py39hbeae22c_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cytoolz                   0.12.0           py39ha30fb19_1    conda-forge
dask                      2022.12.1          pyhd8ed1ab_0    conda-forge
dask-core                 2022.12.1          pyhd8ed1ab_0    conda-forge
datashader                0.14.4             pyh1a96a4e_0    conda-forge
datashape                 0.5.4                      py_1    conda-forge
debugpy                   1.6.7            py39h7a8716b_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
distributed               2022.12.1          pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
fastparquet               2023.2.0         py39h7cc1f47_0    conda-forge
flit-core                 3.8.0              pyhd8ed1ab_0    conda-forge
fonttools                 4.39.3           py39ha30fb19_0    conda-forge
freetype                  2.12.1               h3f81eb7_1    conda-forge
fsspec                    2023.4.0           pyh1a96a4e_0    conda-forge
holoviews                 1.15.4             pyhd8ed1ab_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
importlib-metadata        6.6.0              pyha770c72_0    conda-forge
importlib-resources       5.12.0             pyhd8ed1ab_0    conda-forge
importlib_metadata        6.6.0                hd8ed1ab_0    conda-forge
importlib_resources       5.12.0             pyhd8ed1ab_0    conda-forge
ipykernel                 6.22.0             pyh736e0ef_0    conda-forge
ipython                   8.12.0             pyhd1c38e8_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
jedi                      0.18.2             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge
jupyter_client            8.2.0              pyhd8ed1ab_0    conda-forge
jupyter_core              5.3.0            py39h6e9494a_0    conda-forge
jupyter_events            0.6.3              pyhd8ed1ab_0    conda-forge
jupyter_server            2.5.0              pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.4.4              pyhd8ed1ab_1    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
kiwisolver                1.4.4            py39h92daf61_1    conda-forge
lcms2                     2.15                 h2dcdeff_1    conda-forge
lerc                      4.0.0                hb486fe8_0    conda-forge
libblas                   3.9.0           16_osx64_openblas    conda-forge
libbrotlicommon           1.0.9                hb7f2c08_8    conda-forge
libbrotlidec              1.0.9                hb7f2c08_8    conda-forge
libbrotlienc              1.0.9                hb7f2c08_8    conda-forge
libcblas                  3.9.0           16_osx64_openblas    conda-forge
libcxx                    16.0.2               hd57cbcb_0    conda-forge
libdeflate                1.18                 hac1461d_0    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libgfortran               5.0.0           11_3_0_h97931a8_31    conda-forge
libgfortran5              12.2.0              he409387_31    conda-forge
libjpeg-turbo             2.1.5.1              hb7f2c08_0    conda-forge
liblapack                 3.9.0           16_osx64_openblas    conda-forge
libllvm11                 11.1.0               h8fb7429_5    conda-forge
libopenblas               0.3.21          openmp_h429af6e_3    conda-forge
libpng                    1.6.39               ha978bb4_0    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
libsqlite                 3.40.0               ha978bb4_1    conda-forge
libtiff                   4.5.0                hedf67fa_6    conda-forge
libwebp-base              1.3.0                hb7f2c08_0    conda-forge
libxcb                    1.13              h0d85af4_1004    conda-forge
libzlib                   1.2.13               hfd90126_4    conda-forge
llvm-openmp               16.0.2               hff08bdf_0    conda-forge
llvmlite                  0.39.1           py39had167e2_1    conda-forge
locket                    1.0.0              pyhd8ed1ab_0    conda-forge
lz4                       4.3.2            py39hd0af75a_0    conda-forge
lz4-c                     1.9.4                hf0c8a7f_0    conda-forge
markdown                  3.4.3              pyhd8ed1ab_0    conda-forge
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zstd                      1.5.2                hbc0c0cd_6    conda-forge

@jbednar
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jbednar commented Apr 28, 2023

I think the issue is in Datashader rather than HoloViews since I sometimes see no output returned from executing the pure Datashader code above, but I've included the HoloViews code because it's the only way I've found to reliably reproduce the error.

@jbednar jbednar mentioned this issue Apr 28, 2023
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@ianthomas23
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This is another example of the jupyter_client 8 issue that we have seen many times. For example at holoviz/holoviews#5699 (comment).

It is nothing to do with datashader. Datashader doesn't understand anything about sending/receiving data from a web brower, this is all handled by HoloViews.

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jbednar commented Jul 27, 2023

Agreed. In the past I believe a problem invoking Datashader did lead to empty responses, but in this case I agree it turns out to have been the jupyter_client 8 issue (jupyter/notebook#6748).

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