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dask / distributed

A distributed task scheduler for Dask
https://distributed.dask.org
BSD 3-Clause "New" or "Revised" License
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`distributed` breaks `Jupyter` (both lab and notebook) #3093

Open jolespin opened 5 years ago

jolespin commented 5 years ago

I tried installing datashader which uses distributed as a dependency. I noticed that my Jupyter breaks to the point where I can't even run just 0 to get an output from the cells. The developers of datashader helped me figure out which package changes there were prior and post installation.

I went through the painstaking process of manually installing each of the package versions, opening up jupyter lab and trying to print 0. Installing dask, cloudpickle, distributed broke it. I tried downgrading distributed from 2.4.0 --> 2.3.2 but it was still broken. I reinstalled 2.4.0 then uninstalled via pip uninstall distributed and this fixed my Jupyter.

This conversation has a lot of backstory: https://github.com/pyviz/datashader/issues/790

Here's my software version: 

(soothsayer_testing_env) jespinozlt-osx:~ jespinoz$ sw_vers
ProductName:    Mac OS X
ProductVersion: 10.14.6
BuildVersion:   18G95
Here's my environment specs: ``` (soothsayer_testing_env) jespinozlt-osx:~ jespinoz$ conda info active environment : soothsayer_testing_env active env location : /Users/jespinoz/anaconda3/envs/soothsayer_testing_env shell level : 2 user config file : /Users/jespinoz/.condarc populated config files : /Users/jespinoz/.condarc conda version : 4.7.10 conda-build version : 3.18.8 python version : 3.7.3.final.0 virtual packages : base environment : /Users/jespinoz/anaconda3 (writable) channel URLs : https://conda.anaconda.org/bioconda/osx-64 https://conda.anaconda.org/bioconda/noarch https://conda.anaconda.org/conda-forge/osx-64 https://conda.anaconda.org/conda-forge/noarch https://repo.anaconda.com/pkgs/main/osx-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/osx-64 https://repo.anaconda.com/pkgs/r/noarch https://conda.anaconda.org/jolespin/osx-64 https://conda.anaconda.org/jolespin/noarch package cache : /Users/jespinoz/anaconda3/pkgs /Users/jespinoz/.conda/pkgs envs directories : /Users/jespinoz/anaconda3/envs /Users/jespinoz/.conda/envs platform : osx-64 user-agent : conda/4.7.10 requests/2.22.0 CPython/3.7.3 Darwin/18.7.0 OSX/10.14.6 UID:GID : 3456:63 netrc file : None offline mode : False (soothsayer_testing_env) jespinozlt-osx:~ jespinoz$ conda list # packages in environment at /Users/jespinoz/anaconda3/envs/soothsayer_testing_env: # # Name Version Build Channel _r-mutex 1.0.1 anacondar_1 conda-forge adjusttext 0.7.3.1 py_0 conda-forge appnope 0.1.0 py36_1000 conda-forge astropy 3.2.1 py36h01d97ff_0 conda-forge atomicwrites 1.3.0 py_0 conda-forge attrs 19.1.0 py_0 conda-forge backcall 0.1.0 py_0 conda-forge bids-validator 1.2.4 pypi_0 pypi bioconductor-annotationdbi 1.46.0 r36_1 bioconda bioconductor-biobase 2.44.0 r36h01d97ff_1 bioconda bioconductor-biocgenerics 0.30.0 r36_1 bioconda bioconductor-biomformat 1.12.0 r36_1 bioconda bioconductor-biostrings 2.52.0 r36h01d97ff_1 bioconda bioconductor-edger 3.26.5 r36h6de7cb9_0 bioconda bioconductor-ggtree 1.16.3 r36_0 bioconda bioconductor-go.db 3.8.2 r36_1 bioconda bioconductor-ihw 1.12.0 r36_1 bioconda bioconductor-impute 1.58.0 r36hd44dcd8_1 bioconda bioconductor-iranges 2.18.2 r36h01d97ff_0 bioconda bioconductor-limma 3.40.2 r36h01d97ff_0 bioconda bioconductor-lpsymphony 1.12.0 r36h6de7cb9_1 bioconda bioconductor-metagenomeseq 1.26.2 r36_0 bioconda bioconductor-multtest 2.40.0 r36h01d97ff_1 bioconda bioconductor-philr 1.10.0 r36_1 bioconda bioconductor-phyloseq 1.28.0 r36_1 bioconda bioconductor-preprocesscore 1.46.0 r36h01d97ff_1 bioconda bioconductor-rhdf5 2.28.0 r36h6de7cb9_1 bioconda bioconductor-rhdf5lib 1.6.0 r36h01d97ff_1 bioconda bioconductor-s4vectors 0.22.0 r36h01d97ff_1 bioconda bioconductor-treeio 1.8.1 r36_0 bioconda bioconductor-wrench 1.2.0 r36_1 bioconda bioconductor-xvector 0.24.0 r36h01d97ff_1 bioconda bioconductor-zlibbioc 1.30.0 r36h01d97ff_1 bioconda biom-format 2.1.7 py36h917ab60_1002 conda-forge biopython 1.74 py36h01d97ff_0 conda-forge bleach 3.1.0 pypi_0 pypi bokeh 1.3.4 py36_0 conda-forge bwidget 1.9.11 0 conda-forge bzip2 1.0.8 h01d97ff_1 conda-forge ca-certificates 2019.9.11 hecc5488_0 conda-forge cachecontrol 0.12.5 py_0 conda-forge cairo 1.16.0 h0ab9d94_1001 conda-forge cctools 895 1 conda-forge certifi 2016.9.26 py36_0 conda-forge clang 4.0.1 1 conda-forge clang_osx-64 4.0.1 h1ce6c1d_17 conda-forge clangxx 4.0.1 1 conda-forge clangxx_osx-64 4.0.1 h22b1bf0_17 conda-forge click 7.0 py_0 conda-forge cloudpickle 1.2.2 pypi_0 pypi compiler-rt 4.0.1 hcfea43d_1 curl 7.65.3 ha441bb4_0 cycler 0.10.0 py_1 conda-forge cython 0.29.13 py36h6de7cb9_0 conda-forge dask 2.4.0 pypi_0 pypi dbus 1.13.6 h2f22bb5_0 conda-forge decorator 4.4.0 py_0 conda-forge defusedxml 0.6.0 pypi_0 pypi docopt 0.6.2 pypi_0 pypi entrypoints 0.3 pypi_0 pypi et-xmlfile 1.0.1 pypi_0 pypi ete3 3.1.1 py36_0 bioconda expat 2.2.5 h6de7cb9_1003 conda-forge fastcluster 1.1.25 py36h1702cab_1000 conda-forge fontconfig 2.13.1 h1027ab8_1000 conda-forge freetype 2.10.0 h24853df_1 conda-forge fribidi 1.0.5 h01d97ff_1002 conda-forge fsspec 0.5.1 pypi_0 pypi future 0.17.1 py36_1000 conda-forge gettext 0.19.8.1 h46ab8bc_1002 conda-forge gfortran_osx-64 4.8.5 h22b1bf0_8 conda-forge glib 2.58.3 h9d45998_1002 conda-forge gneiss 0.4.5 py_0 bioconda graphite2 1.3.13 h2098e52_1000 conda-forge graphviz 2.38.0 hc6cc99f_1011 conda-forge gsl 2.4 ha2d443c_1006 conda-forge harfbuzz 2.4.0 h92b87b8_1 conda-forge hdmedians 0.13 py36heacc8b8_1001 conda-forge heapdict 1.0.1 pypi_0 pypi icu 58.2 h0a44026_1000 conda-forge imageio 2.5.0 pypi_0 pypi importlib_metadata 0.23 py36_0 conda-forge ipykernel 5.1.2 pypi_0 pypi ipython 7.8.0 py36h5ca1d4c_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge jdcal 1.4.1 pypi_0 pypi jedi 0.15.1 py36_0 conda-forge jinja2 2.10.1 py_0 conda-forge joblib 0.13.2 py_0 conda-forge jpeg 9c h1de35cc_1001 conda-forge json5 0.8.5 pypi_0 pypi jsonschema 3.0.2 pypi_0 pypi jupyter-client 5.3.3 pypi_0 pypi jupyter-core 4.5.0 pypi_0 pypi jupyterlab 1.1.4 pypi_0 pypi jupyterlab-server 1.0.6 pypi_0 pypi kiwisolver 1.1.0 py36h770b8ee_0 conda-forge krb5 1.16.1 hddcf347_7 ld64 274.2 1 libblas 3.8.0 12_openblas conda-forge libcblas 3.8.0 12_openblas conda-forge libcurl 7.65.3 h051b688_0 libcxx 4.0.1 hcfea43d_1 conda-forge libcxxabi 4.0.1 hcfea43d_1 conda-forge libedit 3.1.20181209 hb402a30_0 libffi 3.2.1 h475c297_4 libgfortran 3.0.1 0 conda-forge libiconv 1.15 h01d97ff_1005 conda-forge liblapack 3.8.0 12_openblas conda-forge libopenblas 0.3.7 hd44dcd8_1 conda-forge libpng 1.6.37 h2573ce8_0 conda-forge libssh2 1.8.2 hcdc9a53_2 conda-forge libtiff 4.0.10 hd08fb8f_1003 conda-forge libxcb 1.13 h1de35cc_1002 conda-forge libxml2 2.9.9 hd80cff7_2 conda-forge libxslt 1.1.33 h33a18ac_0 llvm 4.0.1 1 conda-forge llvm-lto-tapi 4.0.1 1 conda-forge llvm-openmp 9.0.0 h40edb58_0 conda-forge llvmlite 0.29.0 pypi_0 pypi locket 0.2.0 pypi_0 pypi lockfile 0.12.2 py_1 conda-forge lxml 4.4.1 py36h08abf6f_0 conda-forge lz4-c 1.8.3 h6de7cb9_1001 conda-forge make 4.2.1 h1de35cc_2004 conda-forge markupsafe 1.1.1 py36h1de35cc_0 conda-forge matplotlib 3.1.1 py36_1 conda-forge matplotlib-base 3.1.1 py36h3a684a6_1 conda-forge matplotlib-venn 0.11.5 py_1 conda-forge mistune 0.8.4 pypi_0 pypi more-itertools 7.2.0 py_0 conda-forge msgpack-python 0.6.2 py36h770b8ee_0 conda-forge multipledispatch 0.6.0 pypi_0 pypi natsort 6.0.0 py_0 conda-forge nbconvert 5.6.0 pypi_0 pypi nbformat 4.4.0 pypi_0 pypi ncurses 6.1 h0a44026_1 networkx 2.3 py_0 conda-forge nibabel 2.5.1 pypi_0 pypi nilearn 0.5.2 pypi_0 pypi nose 1.3.7 py36_1002 conda-forge notebook 6.0.1 pypi_0 pypi num2words 0.5.10 pypi_0 pypi numba 0.45.1 pypi_0 pypi numpy 1.17.2 py36h6b0580a_0 conda-forge olefile 0.46 py_0 conda-forge openpyxl 2.6.3 pypi_0 pypi openssl 1.1.1c h01d97ff_0 conda-forge packaging 19.2 py_0 conda-forge palettable 3.3.0 py_0 conda-forge pandas 0.25.1 py36h86efe34_0 conda-forge pandocfilters 1.4.2 pypi_0 pypi pango 1.42.4 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py_0 conda-forge pytest-openfiles 0.4.0 py_0 conda-forge pytest-remotedata 0.3.1 py_0 conda-forge python 3.6.9 h359304d_0 python-dateutil 2.8.0 py_0 conda-forge python-louvain 0.13 pypi_0 pypi python-ternary 1.0.6 py_0 conda-forge pytz 2019.2 py_0 conda-forge pywavelets 1.0.3 pypi_0 pypi pyyaml 5.1.2 py36h01d97ff_0 conda-forge pyzmq 18.1.0 pypi_0 pypi qt 5.9.7 h93ee506_2 conda-forge r-acepack 1.4.1 r36haf69682_1004 conda-forge r-ade4 1.7_13 r36h159158b_1001 conda-forge r-ape 5.3 r36hf99fc2c_1 conda-forge r-askpass 1.0 r36h1de35cc_0 r r-assertthat 0.2.1 r36h6115d3f_0 r r-backports 1.1.4 r36h46e59ec_0 r r-base 3.6.1 hcb44179_0 r r-base64enc 0.1_3 r36h159158b_1003 conda-forge r-bh 1.69.0_1 r36h6115d3f_0 r r-bit 1.1_14 r36h46e59ec_0 r r-bit64 0.9_7 r36h46e59ec_0 r r-bitops 1.0_6 r36h159158b_1003 conda-forge r-blob 1.1.1 r36h6115d3f_0 r r-callr 3.2.0 r36h6115d3f_0 r r-catools 1.17.1.2 r36hf99fc2c_1 conda-forge r-checkmate 1.9.4 r36h159158b_1 conda-forge r-cli 1.1.0 r36h6115d3f_0 r r-clipr 0.6.0 r36h6115d3f_0 r r-clisymbols 1.2.0 r36h6115d3f_0 r r-cluster 2.1.0 r36haf69682_2 conda-forge r-codetools 0.2_16 r36h6115d3f_1001 conda-forge r-colorspace 1.4_1 r36h159158b_1 conda-forge r-crayon 1.3.4 r36h6115d3f_0 r r-curl 3.3 r36h46e59ec_0 r r-data.table 1.12.2 r36h159158b_1 conda-forge r-dbi 1.0.0 r36h6115d3f_0 r r-dbplyr 1.4.0 r36h6115d3f_0 r r-deoptimr 1.0_8 r36h6115d3f_1002 conda-forge r-desc 1.2.0 r36h6115d3f_0 r r-devtools 2.0.2 r36h6115d3f_0 r r-digest 0.6.18 r36h46e59ec_0 r r-doparallel 1.0.15 r36h6115d3f_0 conda-forge r-dplyr 0.8.0.1 r36h466af19_0 r r-dynamictreecut 1.63_1 r36h6115d3f_1002 conda-forge r-evaluate 0.14 r36h6115d3f_1 conda-forge r-fansi 0.4.0 r36h46e59ec_0 r r-fastcluster 1.1.25 r36ha90c164_1002 conda-forge r-fastmatch 1.1_0 r36h159158b_1004 conda-forge r-fdrtool 1.2.15 r36h159158b_1002 conda-forge r-fit.models 0.5_14 r36h6115d3f_1002 conda-forge r-foreach 1.4.7 r36h6115d3f_0 conda-forge r-foreign 0.8_72 r36h159158b_0 conda-forge r-formula 1.2_3 r36h6115d3f_1002 conda-forge r-fs 1.2.7 r36h466af19_0 r r-gdata 2.18.0 r36h6115d3f_1002 conda-forge r-ggplot2 3.2.1 r36h6115d3f_0 conda-forge r-gh 1.0.1 r36h6115d3f_0 r r-git2r 0.25.2 r36h46e59ec_0 r r-glmnet 2.0_18 r36haf69682_2 conda-forge r-glue 1.3.1 r36h46e59ec_0 r r-gplots 3.0.1.1 r36h6115d3f_1 conda-forge r-gridextra 2.3 r36h6115d3f_1002 conda-forge r-gtable 0.3.0 r36h6115d3f_2 conda-forge r-gtools 3.8.1 r36h159158b_1003 conda-forge r-highr 0.8 r36h6115d3f_1 conda-forge r-hmisc 4.2_0 r36haf69682_2 conda-forge r-htmltable 1.13.2 r36h6115d3f_0 conda-forge r-htmltools 0.3.6 r36h6de7cb9_1003 conda-forge r-htmlwidgets 1.3 r36h6115d3f_1001 conda-forge r-httr 1.4.0 r36h6115d3f_0 r r-igraph 1.2.4.1 r36h75781db_2 conda-forge r-ini 0.3.1 r36h6115d3f_0 r r-iterators 1.0.12 r36h6115d3f_0 conda-forge r-jsonlite 1.6 r36h46e59ec_0 r r-kernsmooth 2.23_15 r36haf69682_1004 conda-forge r-knitr 1.25 r36h6115d3f_0 conda-forge r-labeling 0.3 r36h6115d3f_1002 conda-forge r-lattice 0.20_38 r36h159158b_1002 conda-forge r-latticeextra 0.6_28 r36h6115d3f_1002 conda-forge r-lazyeval 0.2.2 r36h159158b_1 conda-forge r-locfit 1.5_9.1 r36h01d97ff_1004 conda-forge r-magrittr 1.5 r36h6115d3f_4 r r-markdown 1.1 r36h159158b_0 conda-forge r-mass 7.3_51.4 r36h159158b_1 conda-forge r-matrix 1.2_17 r36h159158b_1 conda-forge r-matrixstats 0.55.0 r36h159158b_0 conda-forge r-memoise 1.1.0 r36h6115d3f_0 r r-mgcv 1.8_29 r36h159158b_0 conda-forge r-mime 0.6 r36h46e59ec_0 r r-munsell 0.5.0 r36h6115d3f_1002 conda-forge r-mvtnorm 1.0_11 r36haf69682_2 conda-forge r-nlme 3.1_141 r36haf69682_1 conda-forge r-nnet 7.3_12 r36h159158b_1003 conda-forge r-openssl 1.3 r36h46e59ec_0 r r-pcapp 1.9_73 r36hf99fc2c_1001 conda-forge r-permute 0.9_5 r36_1 conda-forge r-phangorn 2.5.5 r36hf99fc2c_1 conda-forge r-pillar 1.3.1 r36h6115d3f_0 r r-pkgbuild 1.0.3 r36h6115d3f_0 r r-pkgconfig 2.0.2 r36h6115d3f_0 r r-pkgload 1.0.2 r36h466af19_0 r r-plogr 0.2.0 r36h6115d3f_0 r r-plyr 1.8.4 r36hf99fc2c_1003 conda-forge r-prettyunits 1.0.2 r36h6115d3f_0 r r-processx 3.3.0 r36h46e59ec_0 r r-ps 1.3.0 r36h46e59ec_0 r r-purrr 0.3.2 r36h46e59ec_0 r r-quadprog 1.5_7 r36haf69682_2 conda-forge r-r6 2.4.0 r36h6115d3f_0 r r-rcmdcheck 1.3.2 r36h6115d3f_0 r r-rcolorbrewer 1.1_2 r36h6115d3f_1002 conda-forge r-rcpp 1.0.1 r36h466af19_0 r r-remotes 2.0.4 r36h6115d3f_0 r r-reshape2 1.4.3 r36hf99fc2c_1004 conda-forge r-rlang 0.3.4 r36h46e59ec_0 r r-robust 0.4_18.1 r36haf69682_2 conda-forge r-robustbase 0.93_5 r36haf69682_2 conda-forge r-rpart 4.1_15 r36h159158b_1 conda-forge r-rprojroot 1.3_2 r36h6115d3f_0 r r-rrcov 1.4_7 r36haf69682_2 conda-forge r-rsqlite 2.1.1 r36h466af19_0 r r-rstudioapi 0.10 r36h6115d3f_0 r r-rvcheck 0.1.3 r36_1001 conda-forge r-scales 1.0.0 r36hf99fc2c_1002 conda-forge r-sessioninfo 1.1.1 r36h6115d3f_0 r r-slam 0.1_45 r36h159158b_1 conda-forge r-stringi 1.4.3 r36h466af19_0 r r-stringr 1.4.0 r36h6115d3f_1 conda-forge r-survival 2.44_1.1 r36h159158b_1 conda-forge r-sys 3.2 r36h46e59ec_0 r r-tibble 2.1.1 r36h46e59ec_0 r r-tidyr 0.8.3 r36h466af19_0 r r-tidyselect 0.2.5 r36h466af19_0 r r-tidytree 0.2.5 r36h6115d3f_0 conda-forge r-usethis 1.5.0 r36h6115d3f_0 r r-utf8 1.1.4 r36h46e59ec_0 r r-vegan 2.5_6 r36haf69682_0 conda-forge r-viridis 0.5.1 r36h6115d3f_1003 conda-forge r-viridislite 0.3.0 r36h6115d3f_1002 conda-forge r-wgcna 1.68 r36hf99fc2c_1 bioconda r-whisker 0.3_2 r36h6115d3f_4 r r-withr 2.1.2 r36h6115d3f_0 r r-xfun 0.9 r36h6115d3f_0 conda-forge r-xopen 1.0.0 r36h6115d3f_0 r r-yaml 2.2.0 r36h46e59ec_0 r readline 7.0 h1de35cc_5 requests 2.12.5 py36_0 conda-forge rpy2 2.9.4 py36r36h1d22016_0 r scikit-bio 0.5.5 py36h917ab60_1000 conda-forge scikit-image 0.15.0 pypi_0 pypi scikit-learn 0.21.3 py36hd4ffd6c_0 conda-forge scipy 1.3.1 py36hab3da7d_2 conda-forge seaborn 0.9.0 py_1 conda-forge send2trash 1.5.0 pypi_0 pypi setuptools 41.2.0 py36_0 conda-forge sip 4.19.8 py36h0a44026_1000 conda-forge six 1.12.0 py36_1000 conda-forge soothsayer 2019.8 pypi_0 pypi sortedcontainers 2.1.0 pypi_0 pypi sqlalchemy 1.3.8 pypi_0 pypi sqlite 3.29.0 ha441bb4_0 statsmodels 0.10.1 py36heacc8b8_0 conda-forge tblib 1.4.0 pypi_0 pypi templateflow 0.4.1 pypi_0 pypi teneto 0.4.5 pypi_0 pypi terminado 0.8.2 pypi_0 pypi testpath 0.3.1 pypi_0 pypi tk 8.6.8 ha441bb4_0 conda-forge tktable 2.10 h1de35cc_0 toolz 0.10.0 pypi_0 pypi tornado 6.0.3 py36h01d97ff_0 conda-forge tqdm 4.36.1 py_0 conda-forge traitlets 4.3.2 py36_1000 conda-forge tzlocal 2.0.0 py_0 conda-forge wcwidth 0.1.7 py_1 conda-forge webencodings 0.5.1 pypi_0 pypi wheel 0.33.6 py36_0 conda-forge xarray 0.13.0 py_0 conda-forge xorg-kbproto 1.0.7 h1de35cc_1002 conda-forge xorg-libice 1.0.10 h01d97ff_0 conda-forge xorg-libsm 1.2.3 h01d97ff_1000 conda-forge xorg-libx11 1.6.8 h01d97ff_0 conda-forge xorg-libxau 1.0.9 h1de35cc_0 conda-forge xorg-libxdmcp 1.1.3 h01d97ff_0 conda-forge xorg-libxext 1.3.4 h01d97ff_0 conda-forge xorg-libxrender 0.9.10 h01d97ff_1002 conda-forge xorg-renderproto 0.11.1 h1de35cc_1002 conda-forge xorg-xextproto 7.3.0 h1de35cc_1002 conda-forge xorg-xproto 7.0.31 h1de35cc_1007 conda-forge xz 5.2.4 h1de35cc_4 yaml 0.1.7 h1de35cc_1001 conda-forge zict 1.0.0 pypi_0 pypi zipp 0.6.0 py_0 conda-forge zlib 1.2.11 h1de35cc_3 zstd 1.4.0 ha9f0a20_0 conda-forge ```
mrocklin commented 5 years ago

Can you try downgrading to Tornado 5 and see if that resolves the issue? If so, then this is probably something that we would want to raise with Jupyter devs.

On Thu, Sep 26, 2019 at 2:31 PM Josh L. Espinoza notifications@github.com wrote:

I tried installing datashader which uses distributed as a dependency. I noticed that my Jupyter breaks to the point where I can't even run just 0 to get an output from the cells. The developers of datashader helped me figure out which package changes there were prior and post installation.

I went through the painstaking process of manually installing each of the package versions, opening up jupyter lab and trying to print 0. Installing dask, cloudpickle, distributed broke it. I tried downgrading distributed from 2.4.0 --> 2.3.2 but it was still broken. I reinstalled 2.4.0 then uninstalled via pip uninstall distributed and this fixed my Jupyter.

This conversation has a lot of backstory: pyviz/datashader#790 https://github.com/pyviz/datashader/issues/790

Here's my software version:

(soothsayer_testing_env) jespinozlt-osx:~ jespinoz$ sw_vers ProductName: Mac OS X ProductVersion: 10.14.6 BuildVersion: 18G95

Here's my environment specs:

(soothsayer_testing_env) jespinozlt-osx:~ jespinoz$ conda info

 active environment : soothsayer_testing_env
active env location : /Users/jespinoz/anaconda3/envs/soothsayer_testing_env
        shell level : 2
   user config file : /Users/jespinoz/.condarc

populated config files : /Users/jespinoz/.condarc conda version : 4.7.10 conda-build version : 3.18.8 python version : 3.7.3.final.0 virtual packages : base environment : /Users/jespinoz/anaconda3 (writable) channel URLs : https://conda.anaconda.org/bioconda/osx-64 https://conda.anaconda.org/bioconda/noarch https://conda.anaconda.org/conda-forge/osx-64 https://conda.anaconda.org/conda-forge/noarch https://repo.anaconda.com/pkgs/main/osx-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/osx-64 https://repo.anaconda.com/pkgs/r/noarch https://conda.anaconda.org/jolespin/osx-64 https://conda.anaconda.org/jolespin/noarch package cache : /Users/jespinoz/anaconda3/pkgs /Users/jespinoz/.conda/pkgs envs directories : /Users/jespinoz/anaconda3/envs /Users/jespinoz/.conda/envs platform : osx-64 user-agent : conda/4.7.10 requests/2.22.0 CPython/3.7.3 Darwin/18.7.0 OSX/10.14.6 UID:GID : 3456:63 netrc file : None offline mode : False

(soothsayer_testing_env) jespinozlt-osx:~ jespinoz$ conda list

packages in environment at /Users/jespinoz/anaconda3/envs/soothsayer_testing_env:

#

Name Version Build Channel

_r-mutex 1.0.1 anacondar_1 conda-forge adjusttext 0.7.3.1 py_0 conda-forge appnope 0.1.0 py36_1000 conda-forge astropy 3.2.1 py36h01d97ff_0 conda-forge atomicwrites 1.3.0 py_0 conda-forge attrs 19.1.0 py_0 conda-forge backcall 0.1.0 py_0 conda-forge bids-validator 1.2.4 pypi_0 pypi bioconductor-annotationdbi 1.46.0 r36_1 bioconda bioconductor-biobase 2.44.0 r36h01d97ff_1 bioconda bioconductor-biocgenerics 0.30.0 r36_1 bioconda bioconductor-biomformat 1.12.0 r36_1 bioconda bioconductor-biostrings 2.52.0 r36h01d97ff_1 bioconda bioconductor-edger 3.26.5 r36h6de7cb9_0 bioconda bioconductor-ggtree 1.16.3 r36_0 bioconda bioconductor-go.db 3.8.2 r36_1 bioconda bioconductor-ihw 1.12.0 r36_1 bioconda bioconductor-impute 1.58.0 r36hd44dcd8_1 bioconda bioconductor-iranges 2.18.2 r36h01d97ff_0 bioconda bioconductor-limma 3.40.2 r36h01d97ff_0 bioconda bioconductor-lpsymphony 1.12.0 r36h6de7cb9_1 bioconda bioconductor-metagenomeseq 1.26.2 r36_0 bioconda bioconductor-multtest 2.40.0 r36h01d97ff_1 bioconda bioconductor-philr 1.10.0 r36_1 bioconda bioconductor-phyloseq 1.28.0 r36_1 bioconda bioconductor-preprocesscore 1.46.0 r36h01d97ff_1 bioconda bioconductor-rhdf5 2.28.0 r36h6de7cb9_1 bioconda bioconductor-rhdf5lib 1.6.0 r36h01d97ff_1 bioconda bioconductor-s4vectors 0.22.0 r36h01d97ff_1 bioconda bioconductor-treeio 1.8.1 r36_0 bioconda bioconductor-wrench 1.2.0 r36_1 bioconda bioconductor-xvector 0.24.0 r36h01d97ff_1 bioconda bioconductor-zlibbioc 1.30.0 r36h01d97ff_1 bioconda biom-format 2.1.7 py36h917ab60_1002 conda-forge biopython 1.74 py36h01d97ff_0 conda-forge bleach 3.1.0 pypi_0 pypi bokeh 1.3.4 py36_0 conda-forge bwidget 1.9.11 0 conda-forge bzip2 1.0.8 h01d97ff_1 conda-forge ca-certificates 2019.9.11 hecc5488_0 conda-forge cachecontrol 0.12.5 py_0 conda-forge cairo 1.16.0 h0ab9d94_1001 conda-forge cctools 895 1 conda-forge certifi 2016.9.26 py36_0 conda-forge clang 4.0.1 1 conda-forge clang_osx-64 4.0.1 h1ce6c1d_17 conda-forge clangxx 4.0.1 1 conda-forge clangxx_osx-64 4.0.1 h22b1bf0_17 conda-forge click 7.0 py_0 conda-forge cloudpickle 1.2.2 pypi_0 pypi compiler-rt 4.0.1 hcfea43d_1 curl 7.65.3 ha441bb4_0 cycler 0.10.0 py_1 conda-forge cython 0.29.13 py36h6de7cb9_0 conda-forge dask 2.4.0 pypi_0 pypi dbus 1.13.6 h2f22bb5_0 conda-forge decorator 4.4.0 py_0 conda-forge defusedxml 0.6.0 pypi_0 pypi docopt 0.6.2 pypi_0 pypi entrypoints 0.3 pypi_0 pypi et-xmlfile 1.0.1 pypi_0 pypi ete3 3.1.1 py36_0 bioconda expat 2.2.5 h6de7cb9_1003 conda-forge fastcluster 1.1.25 py36h1702cab_1000 conda-forge fontconfig 2.13.1 h1027ab8_1000 conda-forge freetype 2.10.0 h24853df_1 conda-forge fribidi 1.0.5 h01d97ff_1002 conda-forge fsspec 0.5.1 pypi_0 pypi future 0.17.1 py36_1000 conda-forge gettext 0.19.8.1 h46ab8bc_1002 conda-forge gfortran_osx-64 4.8.5 h22b1bf0_8 conda-forge glib 2.58.3 h9d45998_1002 conda-forge gneiss 0.4.5 py_0 bioconda graphite2 1.3.13 h2098e52_1000 conda-forge graphviz 2.38.0 hc6cc99f_1011 conda-forge gsl 2.4 ha2d443c_1006 conda-forge harfbuzz 2.4.0 h92b87b8_1 conda-forge hdmedians 0.13 py36heacc8b8_1001 conda-forge heapdict 1.0.1 pypi_0 pypi icu 58.2 h0a44026_1000 conda-forge imageio 2.5.0 pypi_0 pypi importlib_metadata 0.23 py36_0 conda-forge ipykernel 5.1.2 pypi_0 pypi ipython 7.8.0 py36h5ca1d4c_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge jdcal 1.4.1 pypi_0 pypi jedi 0.15.1 py36_0 conda-forge jinja2 2.10.1 py_0 conda-forge joblib 0.13.2 py_0 conda-forge jpeg 9c h1de35cc_1001 conda-forge json5 0.8.5 pypi_0 pypi jsonschema 3.0.2 pypi_0 pypi jupyter-client 5.3.3 pypi_0 pypi jupyter-core 4.5.0 pypi_0 pypi jupyterlab 1.1.4 pypi_0 pypi jupyterlab-server 1.0.6 pypi_0 pypi kiwisolver 1.1.0 py36h770b8ee_0 conda-forge krb5 1.16.1 hddcf347_7 ld64 274.2 1 libblas 3.8.0 12_openblas conda-forge libcblas 3.8.0 12_openblas conda-forge libcurl 7.65.3 h051b688_0 libcxx 4.0.1 hcfea43d_1 conda-forge libcxxabi 4.0.1 hcfea43d_1 conda-forge libedit 3.1.20181209 hb402a30_0 libffi 3.2.1 h475c297_4 libgfortran 3.0.1 0 conda-forge libiconv 1.15 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nbformat 4.4.0 pypi_0 pypi ncurses 6.1 h0a44026_1 networkx 2.3 py_0 conda-forge nibabel 2.5.1 pypi_0 pypi nilearn 0.5.2 pypi_0 pypi nose 1.3.7 py36_1002 conda-forge notebook 6.0.1 pypi_0 pypi num2words 0.5.10 pypi_0 pypi numba 0.45.1 pypi_0 pypi numpy 1.17.2 py36h6b0580a_0 conda-forge olefile 0.46 py_0 conda-forge openpyxl 2.6.3 pypi_0 pypi openssl 1.1.1c h01d97ff_0 conda-forge packaging 19.2 py_0 conda-forge palettable 3.3.0 py_0 conda-forge pandas 0.25.1 py36h86efe34_0 conda-forge pandocfilters 1.4.2 pypi_0 pypi pango 1.42.4 h6691c8e_1 conda-forge param 1.9.1 pypi_0 pypi parso 0.5.1 py_0 conda-forge partd 1.0.0 pypi_0 pypi patsy 0.5.1 py_0 conda-forge pcre 8.43 h0a44026_0 pexpect 4.7.0 py36_0 conda-forge pickleshare 0.7.5 py36_1000 conda-forge pillow 6.1.0 py36hb68e598_0 pip 19.2.3 py36_0 conda-forge pixman 0.38.0 h01d97ff_1003 conda-forge pluggy 0.12.0 py_0 conda-forge prometheus-client 0.7.1 pypi_0 pypi prompt_toolkit 2.0.9 py_0 conda-forge psutil 5.6.3 py36h01d97ff_0 conda-forge pthread-stubs 0.4 h1de35cc_1001 conda-forge ptyprocess 0.6.0 py_1001 conda-forge py 1.8.0 py_0 conda-forge pybids 0.9.4 pypi_0 pypi pyct 0.4.6 pypi_0 pypi pydot 1.4.1 py36_1001 conda-forge pygments 2.4.2 py_0 conda-forge pygraphviz 1.5 py36h01d97ff_1001 conda-forge pyhamcrest 1.9.0 py_2 conda-forge pyparsing 2.4.2 py_0 conda-forge pyqt 5.9.2 py36h2a560b1_4 conda-forge pyrsistent 0.15.4 pypi_0 pypi pytest 5.1.2 py36_0 conda-forge pytest-arraydiff 0.3 py_0 conda-forge pytest-astropy 0.5.0 py_0 conda-forge pytest-doctestplus 0.4.0 py_0 conda-forge pytest-openfiles 0.4.0 py_0 conda-forge pytest-remotedata 0.3.1 py_0 conda-forge python 3.6.9 h359304d_0 python-dateutil 2.8.0 py_0 conda-forge python-louvain 0.13 pypi_0 pypi python-ternary 1.0.6 py_0 conda-forge pytz 2019.2 py_0 conda-forge pywavelets 1.0.3 pypi_0 pypi pyyaml 5.1.2 py36h01d97ff_0 conda-forge pyzmq 18.1.0 pypi_0 pypi qt 5.9.7 h93ee506_2 conda-forge r-acepack 1.4.1 r36haf69682_1004 conda-forge r-ade4 1.7_13 r36h159158b_1001 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r36h6115d3f_0 r r-yaml 2.2.0 r36h46e59ec_0 r readline 7.0 h1de35cc_5 requests 2.12.5 py36_0 conda-forge rpy2 2.9.4 py36r36h1d22016_0 r scikit-bio 0.5.5 py36h917ab60_1000 conda-forge scikit-image 0.15.0 pypi_0 pypi scikit-learn 0.21.3 py36hd4ffd6c_0 conda-forge scipy 1.3.1 py36hab3da7d_2 conda-forge seaborn 0.9.0 py_1 conda-forge send2trash 1.5.0 pypi_0 pypi setuptools 41.2.0 py36_0 conda-forge sip 4.19.8 py36h0a44026_1000 conda-forge six 1.12.0 py36_1000 conda-forge soothsayer 2019.8 pypi_0 pypi sortedcontainers 2.1.0 pypi_0 pypi sqlalchemy 1.3.8 pypi_0 pypi sqlite 3.29.0 ha441bb4_0 statsmodels 0.10.1 py36heacc8b8_0 conda-forge tblib 1.4.0 pypi_0 pypi templateflow 0.4.1 pypi_0 pypi teneto 0.4.5 pypi_0 pypi terminado 0.8.2 pypi_0 pypi testpath 0.3.1 pypi_0 pypi tk 8.6.8 ha441bb4_0 conda-forge tktable 2.10 h1de35cc_0 toolz 0.10.0 pypi_0 pypi tornado 6.0.3 py36h01d97ff_0 conda-forge tqdm 4.36.1 py_0 conda-forge traitlets 4.3.2 py36_1000 conda-forge tzlocal 2.0.0 py_0 conda-forge wcwidth 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jolespin commented 5 years ago

I just tried installing pip install tornado==5 and I'm still getting the same hang up.

Can I literally just copy and paste my original post to https://github.com/jupyter/jupyter_core ?

mrocklin commented 5 years ago

Installing dask, cloudpickle, distributed broke it. I tried downgrading distributed from 2.4.0 --> 2.3.2 but it was still broken. I reinstalled 2.4.0 then uninstalled via pip uninstall distributed and this fixed my Jupyter

It would be good to know more precisely where the issue is. With the information you have now it's clear that a problem exists, but unfortunately it's not clear what the problem is or how to fix it.

Does the problem arise if you only install dask, or only install cloudpickle, or only install tornado? If you install all of distributed's dependencies, but not distributed, does it still work?

mrocklin commented 5 years ago

Can I literally just copy and paste my original post to https://github.com/jupyter/jupyter_core ?

I don't know what the Jupyter devs prefer here unfortunately.

mrocklin commented 5 years ago

Your environment is also quite large. It would be very valuable to get the smallest possible environment that reproduces this issue. That would make it much more likely that we could get someone to help us.

jolespin commented 5 years ago

I think it works because I installed dask, cloudpickle, and distributed then it wasn't working. I uninstalled distributed and left the other 2, then the problem was fixed.

Is there anything else I can try or print out before I move on from this today?

mrocklin commented 5 years ago

Is there anything else I can try or print out before I move on from this today?

Creating a minimal environment is probably the most important step to identify the problem.

This might be either a command like the following:

conda create -n jupyter-stalls jupyter distributed=2.4 ...

Or a conda environment file such that if a maintainer creates that environment, they too will see the same error. Ideally this environment doesn't include many packages that are unrelated to the error.

jolespin commented 5 years ago

Yup, here's the environment file: https://github.com/jolespin/soothsayer/blob/master/install/soothsayer_py36_v2019.08.osx.yml

conda env create --name soothsayer_testing_env --file <> --yes

Interesting, so I just installed the minimal environment and it's working with jupyter and distributed together.

conda environment details ``` (jupyter-stalls) jespinozlt-osx:~ jespinoz$ conda info active environment : jupyter-stalls active env location : /Users/jespinoz/anaconda3/envs/jupyter-stalls shell level : 2 user config file : /Users/jespinoz/.condarc populated config files : /Users/jespinoz/.condarc conda version : 4.7.10 conda-build version : 3.18.8 python version : 3.7.3.final.0 virtual packages : base environment : /Users/jespinoz/anaconda3 (writable) channel URLs : https://conda.anaconda.org/bioconda/osx-64 https://conda.anaconda.org/bioconda/noarch https://conda.anaconda.org/conda-forge/osx-64 https://conda.anaconda.org/conda-forge/noarch https://repo.anaconda.com/pkgs/main/osx-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/osx-64 https://repo.anaconda.com/pkgs/r/noarch https://conda.anaconda.org/jolespin/osx-64 https://conda.anaconda.org/jolespin/noarch package cache : /Users/jespinoz/anaconda3/pkgs /Users/jespinoz/.conda/pkgs envs directories : /Users/jespinoz/anaconda3/envs /Users/jespinoz/.conda/envs platform : osx-64 user-agent : conda/4.7.10 requests/2.22.0 CPython/3.7.3 Darwin/18.7.0 OSX/10.14.6 UID:GID : 3456:63 netrc file : None offline mode : False (jupyter-stalls) jespinozlt-osx:~ jespinoz$ conda list # packages in environment at /Users/jespinoz/anaconda3/envs/jupyter-stalls: # # Name Version Build Channel appnope 0.1.0 py36_1000 conda-forge attrs 19.1.0 py_0 conda-forge backcall 0.1.0 py_0 conda-forge bleach 1.4.2 py36_0 bioconda ca-certificates 2019.9.11 hecc5488_0 conda-forge certifi 2016.9.26 py36_0 conda-forge click 7.0 py_0 conda-forge cloudpickle 1.2.2 py_0 conda-forge cytoolz 0.10.0 py36h01d97ff_0 conda-forge dask-core 2.4.0 py_0 conda-forge dbus 1.13.6 h2f22bb5_0 conda-forge decorator 4.4.0 py_0 conda-forge defusedxml 0.5.0 py_1 conda-forge distributed 2.4.0 py_0 conda-forge entrypoints 0.3 py36_1000 conda-forge expat 2.2.5 h6de7cb9_1003 conda-forge gettext 0.19.8.1 h46ab8bc_1002 conda-forge glib 2.58.3 h9d45998_1002 conda-forge heapdict 1.0.1 py_0 conda-forge html5lib 1.0.1 py_0 conda-forge icu 64.2 h6de7cb9_1 conda-forge ipykernel 5.1.2 py36h5ca1d4c_0 conda-forge ipython 7.8.0 py36h5ca1d4c_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge ipywidgets 7.5.1 py_0 conda-forge jedi 0.15.1 py36_0 conda-forge jinja2 2.10.1 py_0 conda-forge jpeg 9c h1de35cc_1001 conda-forge json5 0.8.5 pypi_0 pypi jsonschema 3.0.2 py36_0 conda-forge jupyter 1.0.0 py_2 conda-forge jupyter_client 5.3.3 py36_1 conda-forge jupyter_console 6.0.0 py_0 conda-forge jupyter_core 4.4.0 py_0 conda-forge jupyterlab 1.1.4 pypi_0 pypi jupyterlab-server 1.0.6 pypi_0 pypi libcxx 9.0.0 0 conda-forge libcxxabi 9.0.0 0 conda-forge libffi 3.2.1 1 bioconda libiconv 1.15 h01d97ff_1005 conda-forge libpng 1.6.37 h2573ce8_0 conda-forge libsodium 1.0.17 h01d97ff_0 conda-forge markupsafe 1.1.1 py36h1de35cc_0 conda-forge mistune 0.8.4 py36h1de35cc_1000 conda-forge msgpack-python 0.6.2 py36h770b8ee_0 conda-forge nbconvert 5.6.0 py36_1 conda-forge nbformat 4.4.0 py_1 conda-forge ncurses 6.1 h0a44026_1002 conda-forge notebook 6.0.1 py36_0 conda-forge openssl 1.1.1c h01d97ff_0 conda-forge pandoc 2.7.3 0 conda-forge pandocfilters 1.4.2 py_1 conda-forge parso 0.5.1 py_0 conda-forge pcre 8.41 h0a44026_1003 conda-forge pexpect 4.7.0 py36_0 conda-forge pickleshare 0.7.5 py36_1000 conda-forge pip 19.2.3 py36_0 conda-forge prometheus_client 0.7.1 py_0 conda-forge prompt_toolkit 2.0.9 py_0 conda-forge psutil 5.6.3 py36h01d97ff_0 conda-forge ptyprocess 0.6.0 py_1001 conda-forge pygments 2.4.2 py_0 conda-forge pyqt 5.9.2 py36h2a560b1_4 conda-forge pyrsistent 0.15.4 py36h01d97ff_0 conda-forge python 3.6.7 h94afb7f_1005 conda-forge python-dateutil 2.8.0 py_0 conda-forge pyyaml 5.1.2 py36h01d97ff_0 conda-forge pyzmq 18.1.0 py36hee98d25_0 conda-forge qt 5.9.7 h8cf7e54_3 conda-forge qtconsole 4.5.5 py_0 conda-forge readline 8.0 hcfe32e1_0 conda-forge send2trash 1.5.0 py_0 conda-forge setuptools 41.2.0 py36_0 conda-forge sip 4.19.8 py36h0a44026_1000 conda-forge six 1.12.0 py36_1000 conda-forge sortedcontainers 2.1.0 py_0 conda-forge sqlite 3.29.0 hb7d70f7_1 conda-forge tblib 1.4.0 py_0 conda-forge terminado 0.8.2 py36_0 conda-forge testpath 0.4.2 py_1001 conda-forge tk 8.6.9 h2573ce8_1003 conda-forge toolz 0.10.0 py_0 conda-forge tornado 6.0.3 py36h01d97ff_0 conda-forge traitlets 4.3.2 py36_1000 conda-forge wcwidth 0.1.7 py_1 conda-forge webencodings 0.5.1 py_1 conda-forge wheel 0.33.6 py36_0 conda-forge widgetsnbextension 3.5.1 py36_0 conda-forge xz 5.2.4 h1de35cc_1001 conda-forge yaml 0.1.7 h1de35cc_1001 conda-forge zeromq 4.3.2 h6de7cb9_2 conda-forge zict 1.0.0 py_0 conda-forge zlib 1.2.11 h01d97ff_1006 conda-forge ```
mrocklin commented 5 years ago

Right, so now the question is what else is going on with all of the packages in your personal environment file. Ideally we would find the minimal environment that recreates the error.

mrocklin commented 5 years ago

Any update here @jolespin ?

jolespin commented 5 years ago

I'm not sure how to go about doing this besides manually installing each package one by one and then running jupyter.

mrocklin commented 5 years ago

That is an approach. I agree that it would take a while, but it's probably much faster than trying to figure out what's going wrong by looking at the code.

Alterenatively you could create an environment file that you know fails, and then remove most of the packages that you think shouldn't affect it, try again, and then do a bit of binary search, removing or adding back in sets of packages. This is still tedious, but at least it's O(log(n)) tedious rather than O(n) tedious :)