Closed jmakov closed 9 months ago
hoxbro
commented
9 months ago Is it possible to give the entire environment with conda env export or pip list?
It seems to be a numba related problem, as the error comes from a simple import import numba as nb. Maybe related to a simple mismatch of dependencies (likely numpy).
jmakov
commented
9 months ago name: quantlab
channels:
- defaults
- conda-forge
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- aiohttp=3.8.5=py39hd1e30aa_0
- aiohttp-cors=0.7.0=py_0
- aiosignal=1.3.1=pyhd8ed1ab_0
- anyio=4.0.0=pyhd8ed1ab_0
- argon2-cffi=23.1.0=pyhd8ed1ab_0
- argon2-cffi-bindings=21.2.0=py39hb9d737c_3
- arrow=1.2.3=pyhd8ed1ab_0
- asttokens=2.4.0=pyhd8ed1ab_0
- async-lru=2.0.4=pyhd8ed1ab_0
- async-timeout=4.0.3=pyhd8ed1ab_0
- attrs=23.1.0=pyh71513ae_1
- aws-c-auth=0.7.3=he2921ad_3
- aws-c-cal=0.6.2=hc309b26_0
- aws-c-common=0.9.0=hd590300_0
- aws-c-compression=0.2.17=h4d4d85c_2
- aws-c-event-stream=0.3.2=h2e3709c_0
- aws-c-http=0.7.12=hc865f51_1
- aws-c-io=0.13.32=h1a03231_3
- aws-c-mqtt=0.9.5=h3a0376c_1
- aws-c-s3=0.3.17=h1678ad6_0
- aws-c-sdkutils=0.1.12=h4d4d85c_1
- aws-checksums=0.1.17=h4d4d85c_1
- aws-crt-cpp=0.23.1=hffbee3f_1
- aws-sdk-cpp=1.11.156=h8bde0db_1
- babel=2.12.1=pyhd8ed1ab_1
- backcall=0.2.0=pyh9f0ad1d_0
- backports=1.0=pyhd8ed1ab_3
- backports.functools_lru_cache=1.6.5=pyhd8ed1ab_0
- beautifulsoup4=4.12.2=pyha770c72_0
- bleach=6.0.0=pyhd8ed1ab_0
- blessed=1.19.1=pyhe4f9e05_2
- bokeh=3.2.2=pyhd8ed1ab_0
- brotli=1.1.0=hd590300_0
- brotli-bin=1.1.0=hd590300_0
- brotli-python=1.1.0=py39h3d6467e_0
- bzip2=1.0.8=h7f98852_4
- c-ares=1.19.1=hd590300_0
- ca-certificates=2023.7.22=hbcca054_0
- cached-property=1.5.2=hd8ed1ab_1
- cached_property=1.5.2=pyha770c72_1
- cachetools=5.3.1=pyhd8ed1ab_0
- certifi=2023.7.22=pyhd8ed1ab_0
- cffi=1.15.1=py39he91dace_3
- charset-normalizer=3.2.0=pyhd8ed1ab_0
- click=8.1.7=unix_pyh707e725_0
- cloudpickle=2.2.1=pyhd8ed1ab_0
- colorama=0.4.6=pyhd8ed1ab_0
- colorcet=3.0.1=pyhd8ed1ab_0
- colorful=0.5.4=pyhd8ed1ab_0
- comm=0.1.4=pyhd8ed1ab_0
- contourpy=1.1.0=py39h7633fee_0
- cryptography=41.0.3=py39hd4f0224_0
- cycler=0.11.0=pyhd8ed1ab_0
- dask-core=2023.9.1=pyhd8ed1ab_0
- datashader=0.15.2=pyhd8ed1ab_0
- datashape=0.5.4=py_1
- debugpy=1.7.0=py39h3d6467e_0
- decorator=5.1.1=pyhd8ed1ab_0
- defusedxml=0.7.1=pyhd8ed1ab_0
- distlib=0.3.7=pyhd8ed1ab_0
- entrypoints=0.4=pyhd8ed1ab_0
- exceptiongroup=1.1.3=pyhd8ed1ab_0
- executing=1.2.0=pyhd8ed1ab_0
- filelock=3.12.3=pyhd8ed1ab_0
- fonttools=4.42.1=py39hd1e30aa_0
- fqdn=1.5.1=pyhd8ed1ab_0
- freetype=2.12.1=hca18f0e_1
- frozenlist=1.4.0=py39hd1e30aa_0
- fsspec=2023.9.0=pyh1a96a4e_0
- gflags=2.2.2=he1b5a44_1004
- glog=0.6.0=h6f12383_0
- google-api-core=2.11.1=pyhd8ed1ab_0
- google-auth=2.17.3=pyh1a96a4e_0
- googleapis-common-protos=1.60.0=pyhd8ed1ab_0
- gpustat=1.1.1=pyhd8ed1ab_0
- grpcio=1.46.3=py39h7fbbf82_0
- holoviews=1.17.1=pyhd8ed1ab_0
- hvplot=0.8.4=pyhd8ed1ab_1
- icu=73.2=h59595ed_0
- idna=3.4=pyhd8ed1ab_0
- importlib-metadata=6.8.0=pyha770c72_0
- importlib-resources=6.0.1=pyhd8ed1ab_0
- importlib_metadata=6.8.0=hd8ed1ab_0
- importlib_resources=6.0.1=pyhd8ed1ab_0
- ipykernel=6.25.2=pyh2140261_0
- ipython=8.15.0=pyh0d859eb_0
- ipywidgets=8.1.0=pyhd8ed1ab_0
- isoduration=20.11.0=pyhd8ed1ab_0
- jedi=0.19.0=pyhd8ed1ab_0
- jinja2=3.1.2=pyhd8ed1ab_1
- json5=0.9.14=pyhd8ed1ab_0
- jsonpointer=2.0=py_0
- jsonschema=4.19.0=pyhd8ed1ab_1
- jsonschema-specifications=2023.7.1=pyhd8ed1ab_0
- jsonschema-with-format-nongpl=4.19.0=pyhd8ed1ab_1
- jupyter-lsp=2.2.0=pyhd8ed1ab_0
- jupyter-resource-usage=1.0.1=pyhd8ed1ab_0
- jupyter_client=8.3.1=pyhd8ed1ab_0
- jupyter_core=5.3.1=py39hf3d152e_0
- jupyter_events=0.7.0=pyhd8ed1ab_2
- jupyter_server=2.7.3=pyhd8ed1ab_0
- jupyter_server_terminals=0.4.4=pyhd8ed1ab_1
- jupyterlab=4.0.5=pyhd8ed1ab_0
- jupyterlab-variableinspector=3.0.9=pyhd8ed1ab_0
- jupyterlab_execute_time=3.0.1=pyhd8ed1ab_0
- jupyterlab_pygments=0.2.2=pyhd8ed1ab_0
- jupyterlab_server=2.25.0=pyhd8ed1ab_0
- jupyterlab_widgets=3.0.8=pyhd8ed1ab_0
- keyutils=1.6.1=h166bdaf_0
- kiwisolver=1.4.5=py39h7633fee_0
- krb5=1.21.2=h659d440_0
- lcms2=2.15=haa2dc70_1
- ld_impl_linux-64=2.40=h41732ed_0
- lerc=4.0.0=h27087fc_0
- libabseil=20230802.0=cxx17_h59595ed_3
- libarrow=13.0.0=h1935d02_4_cpu
- libblas=3.9.0=18_linux64_openblas
- libbrotlicommon=1.1.0=hd590300_0
- libbrotlidec=1.1.0=hd590300_0
- libbrotlienc=1.1.0=hd590300_0
- libcblas=3.9.0=18_linux64_openblas
- libcrc32c=1.1.2=h9c3ff4c_0
- libcurl=8.2.1=hca28451_0
- libdeflate=1.18=h0b41bf4_0
- libedit=3.1.20191231=he28a2e2_2
- libev=4.33=h516909a_1
- libevent=2.1.12=hf998b51_1
- libffi=3.4.2=h7f98852_5
- libgcc-ng=13.2.0=h807b86a_0
- libgfortran-ng=13.2.0=h69a702a_0
- libgfortran5=13.2.0=ha4646dd_0
- libgomp=13.2.0=h807b86a_0
- libgoogle-cloud=2.12.0=h8d7e28b_2
- libgrpc=1.57.0=ha4d0f93_1
- libjpeg-turbo=2.1.5.1=h0b41bf4_0
- liblapack=3.9.0=18_linux64_openblas
- libllvm10=10.0.1=he513fc3_3
- libnghttp2=1.52.0=h61bc06f_0
- libnsl=2.0.0=h7f98852_0
- libnuma=2.0.16=h0b41bf4_1
- libopenblas=0.3.24=pthreads_h413a1c8_0
- libpng=1.6.39=h753d276_0
- libprotobuf=4.23.4=hf27288f_6
- libsodium=1.0.18=h36c2ea0_1
- libsqlite=3.43.0=h2797004_0
- libssh2=1.11.0=h0841786_0
- libstdcxx-ng=13.2.0=h7e041cc_0
- libthrift=0.19.0=h8fd135c_0
- libtiff=4.5.1=h8b53f26_1
- libunwind=1.6.2=h9c3ff4c_0
- libutf8proc=2.8.0=h166bdaf_0
- libuuid=2.38.1=h0b41bf4_0
- libuv=1.46.0=hd590300_0
- libwebp-base=1.3.1=hd590300_0
- libxcb=1.15=h0b41bf4_0
- libzlib=1.2.13=hd590300_5
- linkify-it-py=2.0.0=pyhd8ed1ab_0
- llvmlite=0.36.0=py39h1bbdace_0
- locket=1.0.0=pyhd8ed1ab_0
- lz4-c=1.9.4=hcb278e6_0
- markdown=3.4.4=pyhd8ed1ab_0
- markdown-it-py=3.0.0=pyhd8ed1ab_0
- markupsafe=2.1.3=py39hd1e30aa_0
- matplotlib-base=3.7.2=py39h0126182_0
- matplotlib-inline=0.1.6=pyhd8ed1ab_0
- mdit-py-plugins=0.4.0=pyhd8ed1ab_0
- mdurl=0.1.0=pyhd8ed1ab_0
- mistune=3.0.1=pyhd8ed1ab_0
- msgpack-python=1.0.5=py39h4b4f3f3_0
- multidict=6.0.4=py39h72bdee0_0
- multipledispatch=0.6.0=py_0
- munkres=1.1.4=pyh9f0ad1d_0
- nbclient=0.8.0=pyhd8ed1ab_0
- nbconvert-core=7.8.0=pyhd8ed1ab_0
- nbformat=5.9.2=pyhd8ed1ab_0
- ncurses=6.4=hcb278e6_0
- nest-asyncio=1.5.6=pyhd8ed1ab_0
- nodejs=20.6.1=hb753e55_0
- notebook-shim=0.2.3=pyhd8ed1ab_0
- numba=0.53.1=py39ha9443f7_0
- numpy=1.25.2=py39h6183b62_0
- nvidia-ml-py=12.535.108=pyhd8ed1ab_0
- opencensus=0.11.2=pyhd8ed1ab_0
- opencensus-context=0.1.3=py39hf3d152e_1
- openjpeg=2.5.0=hfec8fc6_2
- openssl=3.1.2=hd590300_0
- orc=1.9.0=h52d3b3c_2
- overrides=7.4.0=pyhd8ed1ab_0
- packaging=23.1=pyhd8ed1ab_0
- pandas=2.1.0=py39hddac248_0
- pandocfilters=1.5.0=pyhd8ed1ab_0
- panel=1.2.2=pyhd8ed1ab_0
- param=1.13.0=pyh1a96a4e_0
- parso=0.8.3=pyhd8ed1ab_0
- partd=1.4.0=pyhd8ed1ab_0
- pexpect=4.8.0=pyh1a96a4e_2
- pickleshare=0.7.5=py_1003
- pillow=10.0.0=py39haaeba84_0
- pip=23.2.1=pyhd8ed1ab_0
- pkgutil-resolve-name=1.3.10=pyhd8ed1ab_0
- platformdirs=3.10.0=pyhd8ed1ab_0
- polars=0.19.2=py39h903e532_0
- pooch=1.7.0=pyha770c72_3
- prometheus_client=0.17.1=pyhd8ed1ab_0
- prompt-toolkit=3.0.39=pyha770c72_0
- prompt_toolkit=3.0.39=hd8ed1ab_0
- protobuf=4.23.4=py39h60f6b12_2
- psutil=5.9.5=py39h72bdee0_0
- pthread-stubs=0.4=h36c2ea0_1001
- ptyprocess=0.7.0=pyhd3deb0d_0
- pure_eval=0.2.2=pyhd8ed1ab_0
- py-spy=0.3.14=h87a5ac0_0
- pyarrow=13.0.0=py39h6925388_4_cpu
- pyasn1=0.4.8=py_0
- pyasn1-modules=0.2.7=py_0
- pycparser=2.21=pyhd8ed1ab_0
- pyct=0.4.6=py_0
- pyct-core=0.4.6=py_0
- pydantic=1.10.12=py39hd1e30aa_1
- pygments=2.16.1=pyhd8ed1ab_0
- pyopenssl=23.2.0=pyhd8ed1ab_1
- pyparsing=3.0.9=pyhd8ed1ab_0
- pysocks=1.7.1=pyha2e5f31_6
- python=3.9.18=h0755675_0_cpython
- python-dateutil=2.8.2=pyhd8ed1ab_0
- python-fastjsonschema=2.18.0=pyhd8ed1ab_0
- python-json-logger=2.0.7=pyhd8ed1ab_0
- python-tzdata=2023.3=pyhd8ed1ab_0
- python_abi=3.9=3_cp39
- pytz=2023.3.post1=pyhd8ed1ab_0
- pyu2f=0.1.5=pyhd8ed1ab_0
- pyviz_comms=3.0.0=pyhd8ed1ab_0
- pyyaml=6.0.1=py39hd1e30aa_0
- pyzmq=25.1.1=py39hb257651_0
- ray-core=2.6.3=py39hf5bac6d_1
- ray-dashboard=2.6.3=py39h7a4ae58_1
- ray-default=2.6.3=py39hf3d152e_1
- rdma-core=28.9=h59595ed_1
- re2=2023.03.02=h8c504da_0
- readline=8.2=h8228510_1
- referencing=0.30.2=pyhd8ed1ab_0
- requests=2.31.0=pyhd8ed1ab_0
- rfc3339-validator=0.1.4=pyhd8ed1ab_0
- rfc3986-validator=0.1.1=pyh9f0ad1d_0
- rpds-py=0.10.2=py39h9fdd4d6_0
- rsa=4.9=pyhd8ed1ab_0
- s2n=1.3.51=h06160fa_0
- scipy=1.11.2=py39h6183b62_0
- send2trash=1.8.2=pyh41d4057_0
- setproctitle=1.2.2=py39hb9d737c_2
- setuptools=68.2.2=pyhd8ed1ab_0
- six=1.16.0=pyh6c4a22f_0
- smart_open=6.4.0=pyhd8ed1ab_0
- snappy=1.1.10=h9fff704_0
- sniffio=1.3.0=pyhd8ed1ab_0
- soupsieve=2.5=pyhd8ed1ab_1
- stack_data=0.6.2=pyhd8ed1ab_0
- tbb=2020.3=hfd86e86_0
- terminado=0.17.1=pyh41d4057_0
- tinycss2=1.2.1=pyhd8ed1ab_0
- tk=8.6.12=h27826a3_0
- tomli=2.0.1=pyhd8ed1ab_0
- toolz=0.12.0=pyhd8ed1ab_0
- tornado=6.3.3=py39hd1e30aa_0
- tqdm=4.66.1=pyhd8ed1ab_0
- traitlets=5.9.0=pyhd8ed1ab_0
- typing-extensions=4.7.1=hd8ed1ab_0
- typing_extensions=4.7.1=pyha770c72_0
- typing_utils=0.1.0=pyhd8ed1ab_0
- tzdata=2023c=h71feb2d_0
- uc-micro-py=1.0.1=pyhd8ed1ab_0
- ucx=1.14.1=h64cca9d_4
- unicodedata2=15.0.0=py39hb9d737c_0
- uri-template=1.3.0=pyhd8ed1ab_0
- urllib3=2.0.4=pyhd8ed1ab_0
- virtualenv=20.21.0=pyhd8ed1ab_0
- wcwidth=0.2.6=pyhd8ed1ab_0
- webcolors=1.13=pyhd8ed1ab_0
- webencodings=0.5.1=py_1
- websocket-client=1.6.3=pyhd8ed1ab_0
- wheel=0.41.2=pyhd8ed1ab_0
- widgetsnbextension=4.0.8=pyhd8ed1ab_0
- xarray=2023.7.0=pyhd8ed1ab_0
- xorg-libxau=1.0.11=hd590300_0
- xorg-libxdmcp=1.1.3=h7f98852_0
- xyzservices=2023.7.0=pyhd8ed1ab_0
- xz=5.2.6=h166bdaf_0
- yaml=0.2.5=h7f98852_2
- yarl=1.9.2=py39hd1e30aa_0
- zeromq=4.3.4=h9c3ff4c_1
- zipp=3.16.2=pyhd8ed1ab_0
- zlib=1.2.13=hd590300_5
- zstd=1.5.5=hfc55251_0It is using an old version of numba, which doesn't seem to have the correct numpy pin.
Try this: conda install numba=0.58 -c numba/label/dev
jmakov
commented
9 months ago install numba=0.58 -c numba/label/dev
Yes, that works. Is there a way I can still use env.yaml or do I need to pin numba?
hoxbro
commented
9 months ago I would add a lower pin to numba like this numba >=0.54 , then it should find the correct version of numpy.
jmakov
commented
9 months ago Thanks for the quick feedback!. Is this something that needs to be in the docs under "installing datashader"?
Stack traceback and/or browser JavaScript console output
Traceback (most recent call last): File "", line 1, in
File "/home/johan/mambaforge-pypy3/envs/test/lib/python3.9/site-packages/datashader/init.py", line 8, in
from .core import Canvas # noqa (API import)
File "/home/johan/mambaforge-pypy3/envs/test/lib/python3.9/site-packages/datashader/core.py", line 13, in
from .utils import Dispatcher, ngjit, calc_res, calc_bbox, orient_array, \
File "/home/johan/mambaforge-pypy3/envs/test/lib/python3.9/site-packages/datashader/utils.py", line 8, in
import numba as nb
File "/home/johan/mambaforge-pypy3/envs/test/lib/python3.9/site-packages/numba/init.py", line 43, in
from numba.np.ufunc import (vectorize, guvectorize, threading_layer,
File "/home/johan/mambaforge-pypy3/envs/test/lib/python3.9/site-packages/numba/np/ufunc/init.py", line 3, in
from numba.np.ufunc.decorators import Vectorize, GUVectorize, vectorize, guvectorize
File "/home/johan/mambaforge-pypy3/envs/test/lib/python3.9/site-packages/numba/np/ufunc/decorators.py", line 3, in
from numba.np.ufunc import _internal
SystemError: initialization of _internal failed without raising an exception
Screenshots or screencasts of the bug in action
env.yaml: