Datashader Crashes Kernel on import

[rjgiedt]

Hi, I just installed datashader hoping to use it, but it crashes my kernel when I try to import it both in a notebook and from the terminal. In the terminal I get the following message:

"Assertion failed: (PassInf && "Expected all immutable passes to be initialized"), function addImmutablePass, file /opt/concourse/worker/volumes/live/beb14cc7-dab9-473f-6096-a3a28d4f005a/volume/llvmdev_1526578337017/work/lib/IR/LegacyPassManager.cpp, line 755. Abort trap: 6 "

Software versions are:

Python 3.6.5 absl-py 0.2.2
aiohttp 3.6.2
alabaster 0.7.10
amqp 2.3.2
anaconda-client 1.6.14
anaconda-navigator 1.9.2
anaconda-project 0.8.2
apeer-ometiff-library 1.6.0
appnope 0.1.0
appscript 1.0.1
asgiref 1.1.2
asn1crypto 0.24.0
astor 0.7.1
astroid 1.6.3
astropy 3.0.2
async-timeout 3.0.1
attrs 18.1.0
autobahn 18.6.1
Automat 0.7.0
Babel 2.5.3
backcall 0.1.0
backports.functools-lru-cache 1.6.1
backports.shutil-get-terminal-size 1.0.0
backports.tempfile 1.0
backports.weakref 1.0.post1
bcrypt 3.1.4
beautifulsoup4 4.6.0
billiard 3.5.0.4
bitarray 0.8.1
bkcharts 0.2
blaze 0.11.3
bleach 2.1.3
bokeh 0.12.16
boto 2.48.0
boto3 1.7.58
botocore 1.10.58
Bottleneck 1.2.1
cachetools 2.1.0
celery 4.2.0
certifi 2018.4.16
cffi 1.11.5
channels 1.1.8
chardet 3.0.4
cheroot 6.3.3
CherryPy 11.0.0
click 6.7
click-plugins 1.0.3
cloudpickle 0.5.3
clyent 1.2.2
cmake 3.11.0
colorama 0.3.9
colorcet 2.0.2
conda 4.8.3
conda-build 3.10.5
conda-package-handling 1.6.0
conda-verify 3.4.2
constantly 15.1.0
contextlib2 0.5.5
cryptography 2.2.2
cycler 0.10.0
Cython 0.29.15
cytoolz 0.9.0.1
czifile 2019.7.2
daphne 1.4.2
dask 2.9.2
datashader 0.6.9
datashape 0.5.4
decorator 4.3.0
diskcache 3.0.6
distributed 1.21.8
Django 1.10.8
djangorestframework 3.4.7
docker 3.4.1
docker-pycreds 0.3.0
docutils 0.14
dogpile.cache 0.6.6
entrypoints 0.2.3
enum34 1.1.6
et-xmlfile 1.0.1
fastcache 1.0.2
feather-format 0.4.0
filelock 3.0.4
Flask 1.0.2
Flask-Cors 3.0.4
freetype-py 2.1.0.post1 fsspec 0.6.2
future 0.18.2
gast 0.2.0
gevent 1.3.0
girder 2.5.0
girder-client 2.4.0
girder-worker 0.5.0
girder-worker-utils 0.8.3
glob2 0.6
gmpy2 2.0.8
google 2.0.3
greenlet 0.4.13
grpcio 1.13.0
h5py 2.7.1
hdbscan 0.8.24
hdf5storage 0.1.14
heapdict 1.0.0
histomicstk 0.2.0 /Users/giedtji1/HistomicsTK html5lib 1.0.1
htmlmin 0.1.12
hyperlink 18.0.0
idna 2.6
idna-ssl 1.1.0
imagecodecs-lite 2019.12.3
imageio 2.3.0
imagesize 1.0.0
imbalanced-learn 0.3.3
img-utils 0.0.13
imglyb 0.4.0
importlib-metadata 0.23
imutils 0.5.3
incremental 17.5.0
ipykernel 5.1.3
ipython 7.11.1
ipython-genutils 0.2.0
ipywidgets 7.2.1
isort 4.3.4
itsdangerous 0.24
jaraco.functools 1.20
jdcal 1.4
jedi 0.12.0
jgo 0.5.0
Jinja2 2.10
jmespath 0.9.3
joblib 0.14.1
jsonfield 2.0.2
jsonpickle 0.9.6
jsonschema 2.6.0
jupyter 1.0.0
jupyter-client 5.2.3
jupyter-console 5.2.0
jupyter-core 4.4.0
jupyterlab 0.32.1
jupyterlab-launcher 0.10.5
Keras 2.2.0
Keras-Applications 1.0.2
Keras-Preprocessing 1.0.1
kiwisolver 1.0.1
kombu 4.2.1
large-image 0.3.0 /Users/giedtji1/large_image lazy-object-proxy 1.3.1
libtiff 0.4.2
lifelines 0.17.0
lime 0.1.1.32
llvmlite 0.23.1
lmdb 0.94
locket 0.2.0
lxml 4.2.1
Mako 1.0.7
Markdown 2.6.11
MarkupSafe 1.0
matplotlib 2.2.2
mccabe 0.6.1
missingno 0.4.2
mistune 0.8.3
mkl-fft 1.0.0
mkl-random 1.0.1
more-itertools 4.1.0
mpmath 1.0.0
mrcnn 0.2
msgpack 0.5.6
msgpack-python 0.5.6
multidict 4.7.5
multipledispatch 0.5.0
mypy-extensions 0.3.0
navigator-updater 0.2.1
nb-conda 2.2.1
nb-conda-kernels 2.2.3
nbconvert 5.3.1
nbformat 4.4.0
networkx 1.11
nimfa 1.3.4
nltk 3.3
nose 1.3.7
notebook 5.5.0
numba 0.38.0
numexpr 2.6.5
numpy 1.16.0
numpydoc 0.9.2
odo 0.5.1
olefile 0.45.1
opencv-contrib-python 4.0.0.21
opencv-python 3.4.1.15
openpyxl 2.5.3
openslide-python 1.1.1
openslides 2.2
packaging 17.1
pandas 0.23.0
pandocfilters 1.4.2
param 1.9.3
parso 0.2.0
partd 0.3.8
path.py 11.0.1
pathlib2 2.3.2
patsy 0.5.0
pbr 4.1.0
pep8 1.7.1
pexif 0.15
pexpect 4.5.0
pickleshare 0.7.4
Pillow 5.1.0
pip 20.0.2
pkginfo 1.4.2
plotly 3.10.0
pluggy 0.13.1
ply 3.11
portend 2.3
prompt-toolkit 3.0.3
protobuf 3.11.3
psutil 5.4.5
ptyprocess 0.5.2
py 1.5.3
py-spy 0.3.3
py-wsi 1.1
pyarrow 0.13.0
pycodestyle 2.4.0
pycosat 0.6.3
pycparser 2.18
pycrypto 2.6.1
pyct 0.4.6
pycurl 7.43.0.1
pyflakes 1.6.0
Pygments 2.2.0
PyHamcrest 1.9.0
pyimagej 0.5.0
pyjnius 1.2.1
pylibczi 1.1.1
pylint 1.8.4
pymongo 3.7.0
pyodbc 4.0.23
pyOpenSSL 18.0.0
pyparsing 2.2.0
PyPDF2 1.26.0
PySide2 5.14.0
PySocks 1.6.8
pytest 5.3.1
pytest-arraydiff 0.2
pytest-astropy 0.3.0
pytest-doctestplus 0.1.3
pytest-openfiles 0.3.0
pytest-pylint 0.14.1
pytest-remotedata 0.2.1
python-dateutil 2.6.1
pytz 2018.4
PyWavelets 0.5.2
PyYAML 3.12
pyzmq 17.0.0
QtAwesome 0.4.4
qtconsole 4.3.1
QtPy 1.9.0
ray 0.8.4
redis 3.5.0
requests 2.18.4
requests-toolbelt 0.8.0
retrying 1.3.3
roman 2.0.0
rope 0.10.7
ruamel-yaml 0.15.35
s3transfer 0.1.13
scikit-build 0.7.1
scikit-image 0.14.2
scikit-learn 0.19.1
scipy 1.4.1
scyjava 0.4.0
seaborn 0.8.1
Send2Trash 1.5.0
setuptools 38.7.0
setuptools-scm 2.1.0
Shapely 1.6.4.post1 shiboken2 5.14.0
simplegeneric 0.8.1
singledispatch 3.4.0.3
six 1.11.0
slideseg 1.1
snowballstemmer 1.2.1
sortedcollections 0.6.1
sortedcontainers 1.5.10
Sphinx 1.7.4
sphinxcontrib-websupport 1.0.1
spyder 3.2.8
SQLAlchemy 1.2.7
statsmodels 0.9.0
stevedore 1.28.0
sympy 1.1.1
tables 3.4.3
TBB 0.1
tblib 1.3.2
tempora 1.13
tensorboard 1.9.0
tensorflow 1.9.0
termcolor 1.1.0
terminado 0.8.1
testpath 0.3.1
tf-keras-contrib 2.0.8
tifffile 2019.7.26.2 toolz 0.9.0
tornado 5.0.2
tqdm 4.46.0
traitlets 4.3.2
Twisted 18.7.0
txaio 2.10.0
typing 3.6.4
typing-extensions 3.7.4.2
umap-learn 0.3.10
unicodecsv 0.14.1
untangle 1.1.1
urllib3 1.22
vine 1.1.4
vispy 0.6.4
wcwidth 0.1.7
webencodings 0.5.1
websocket-client 0.48.0
Werkzeug 0.14.1
wheel 0.31.1
widgetsnbextension 3.2.1
wrapt 1.10.11
xarray 0.13.0
xlrd 1.1.0
XlsxWriter 1.0.4
xlwings 0.11.8
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xmltodict 0.12.0
yarl 1.4.2
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zipp 0.6.0
zope.interface 4.5.0

[esc]

@rjgiedt thanks for reporting this on the Numba issue tracker. It looks very similar to: https://github.com/numba/llvmlite/issues/587 - However, it appears as though your Numba and llvmlite versions are a few years old. There are two thing to do next: 1) update both numba and llvmlite and if that doesn't help 2) report back your operating system. Thanks!

[rjgiedt]

Hi,

I upgraded all packages, numba is now at 0.49.0 and llvmlite is at 0.32.0 and am running on macOS Mojave (10.14.6). I repeated the process above, just trying to import datashader and still ran into a kernel shutdown. Thanks so much for the help!

[esc]

@rjgiedt thanks for looking into this. In order to debug this further, could you perhaps share some more details on your Python version, how you obtained it including Numba and llvmlite and what commands you are running to cause the error? I'd like to get to a point where I can reproduce this error to investigate it further, ideally with a self-contained script, so the more details you can include the higher the chance are of being able to create a reproducer. Thanks!

[rjgiedt]

Of course, happy to help.

Python version: 3.6.10

Command to reproduce the error was simply: import datashader as ds

I'm running this via Anaconda on a Jupyter Notebook, packages were installed via conda install/ conda update. Again, running python through my terminal also produces an error "Assertion failed: (PassInf && "Expected all immutable passes to be initialized"), function addImmutablePass, file /opt/concourse/worker/volumes/live/636f0d85-60d4-452d-50e9-ca6ab5111e2d/volume/llvmdev_1560805383854/work/lib/IR/LegacyPassManager.cpp, line 849. Abort trap: 6"

I'll try to do a fresh install on a different mac machine later today to see if I can independently replicate the error on my end as well and will report back anything I find here!

[esc]

@rjgiedt any luck reproducing this on a fresh install?

[rjgiedt]

Hi, yes on a separate install I'm getting the same error, unfortunately. Thanks again for checking into this!

[esc]

@rjgiedt thanks for reporting back, would it be possible to detail how you set up your conda environment and the packages you installed?

[jlstevens]

Are there any updates on this issue? @esc have you managed to reproduce this, or do you need more info from @rjgiedt?

[esc]

@jlstevens thanks for following up, I have not been able to reproduce this yet and am still waiting on additional info.

[kcpevey]

Closing for now since its not reproducible. Happy to reopen with details on how to reproduce including specific conda env involved.