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norse / norse

Deep learning with spiking neural networks (SNNs) in PyTorch.
https://norse.github.io/norse/
GNU Lesser General Public License v3.0
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Undefined Symbol: _ZN3c106detail19maybe_wrap_dim_slowIlEET_S2_S2_b #375

Closed gcervantes8 closed 1 year ago

gcervantes8 commented 1 year ago

Describe the bug I've been getting a strange error when I import Norse:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/local/lib/python3.10/dist-packages/norse/__init__.py", line 4, in <module>
    from . import benchmark, dataset, task, torch, utils
  File "/usr/local/lib/python3.10/dist-packages/norse/torch/__init__.py", line 7, in <module>
    from .models import *
  File "/usr/local/lib/python3.10/dist-packages/norse/torch/models/__init__.py", line 1, in <module>
    from .conv import ConvNet, ConvNet4
  File "/usr/local/lib/python3.10/dist-packages/norse/torch/models/conv.py", line 3, in <module>
    from norse.torch.functional.lif import LIFParameters
  File "/usr/local/lib/python3.10/dist-packages/norse/torch/functional/__init__.py", line 5, in <module>
    from .adjoint.lif_adjoint import (
  File "/usr/local/lib/python3.10/dist-packages/norse/torch/functional/adjoint/lif_adjoint.py", line 4, in <module>
    from norse.torch.functional.lif import (
  File "/usr/local/lib/python3.10/dist-packages/norse/torch/functional/lif.py", line 35, in <module>
    import norse_op
ImportError: /usr/local/lib/python3.10/dist-packages/norse_op.so: undefined symbol: _ZN3c106detail19maybe_wrap_dim_slowIlEET_S2_S2_b

To Reproduce Steps to reproduce the behavior: I was able to reproduce the behavior by running the following commands on a Google Colab environment:

!pip install norse
!pip install lava
!pip install lava-dl
!python -c "import norse"

I found that Norse ends up working up until lava-dl is installed, I believe this changes the Torch installation so this might be way the error is occurring.

Environment

Python 3.10.12
Package                          Version
-------------------------------- ---------------------
absl-py                          1.4.0
aiohttp                          3.8.5
aiosignal                        1.3.1
alabaster                        0.7.13
albumentations                   1.3.1
altair                           4.2.2
annotated-types                  0.5.0
anyio                            3.7.1
appdirs                          1.4.4
argon2-cffi                      23.1.0
argon2-cffi-bindings             21.2.0
array-record                     0.4.1
arviz                            0.15.1
asteval                          0.9.31
astropy                          5.3.2
astunparse                       1.6.3
async-timeout                    4.0.3
attrs                            23.1.0
audioread                        3.0.0
autograd                         1.6.2
Babel                            2.12.1
backcall                         0.2.0
beautifulsoup4                   4.11.2
bleach                           6.0.0
blinker                          1.4
blis                             0.7.10
blosc2                           2.0.0
bokeh                            3.2.2
branca                           0.6.0
build                            0.10.0
CacheControl                     0.13.1
cachetools                       5.3.1
catalogue                        2.0.9
certifi                          2023.7.22
cffi                             1.15.1
chardet                          5.2.0
charset-normalizer               3.2.0
chex                             0.1.7
click                            8.1.7
click-plugins                    1.1.1
cligj                            0.7.2
cloudpickle                      2.2.1
cmake                            3.27.2
cmdstanpy                        1.1.0
colorcet                         3.0.1
colorlover                       0.3.0
community                        1.0.0b1
confection                       0.1.1
cons                             0.4.6
contextlib2                      21.6.0
contourpy                        1.1.0
convertdate                      2.4.0
cryptography                     41.0.3
cufflinks                        0.17.3
cvxopt                           1.3.2
cvxpy                            1.3.2
cycler                           0.11.0
cymem                            2.0.7
Cython                           0.29.36
dask                             2023.8.0
datascience                      0.17.6
db-dtypes                        1.1.1
dbus-python                      1.2.18
debugpy                          1.6.6
decorator                        4.4.2
defusedxml                       0.7.1
distributed                      2023.8.0
distro                           1.7.0
dlib                             19.24.2
dm-tree                          0.1.8
docutils                         0.18.1
dopamine-rl                      4.0.6
duckdb                           0.8.1
earthengine-api                  0.1.364
easydict                         1.10
ecos                             2.0.12
editdistance                     0.6.2
en-core-web-sm                   3.6.0
entrypoints                      0.4
ephem                            4.1.4
et-xmlfile                       1.1.0
etils                            1.4.1
etuples                          0.3.9
exceptiongroup                   1.1.3
fastai                           2.7.12
fastcore                         1.5.29
fastdownload                     0.0.7
fastjsonschema                   2.18.0
fastprogress                     1.0.3
fastrlock                        0.8.1
filelock                         3.12.2
Fiona                            1.9.4.post1
firebase-admin                   5.3.0
Flask                            2.2.5
flatbuffers                      23.5.26
flax                             0.7.2
folium                           0.14.0
fonttools                        4.42.0
frozendict                       2.3.8
frozenlist                       1.4.0
fsspec                           2023.6.0
future                           0.18.3
gast                             0.4.0
gcsfs                            2023.6.0
GDAL                             3.4.3
gdown                            4.6.6
gensim                           4.3.1
geographiclib                    2.0
geopandas                        0.13.2
geopy                            2.3.0
gin-config                       0.5.0
glob2                            0.7
google                           2.0.3
google-api-core                  2.11.1
google-api-python-client         2.84.0
google-auth                      2.17.3
google-auth-httplib2             0.1.0
google-auth-oauthlib             1.0.0
google-cloud-bigquery            3.10.0
google-cloud-bigquery-connection 1.12.1
google-cloud-bigquery-storage    2.22.0
google-cloud-core                2.3.3
google-cloud-datastore           2.15.2
google-cloud-firestore           2.11.1
google-cloud-functions           1.13.2
google-cloud-language            2.9.1
google-cloud-storage             2.8.0
google-cloud-translate           3.11.3
google-colab                     1.0.0
google-crc32c                    1.5.0
google-pasta                     0.2.0
google-resumable-media           2.5.0
googleapis-common-protos         1.60.0
googledrivedownloader            0.4
graphviz                         0.20.1
greenlet                         2.0.2
grpc-google-iam-v1               0.12.6
grpcio                           1.57.0
grpcio-status                    1.48.2
gspread                          3.4.2
gspread-dataframe                3.3.1
gym                              0.25.2
gym-notices                      0.0.8
h5netcdf                         1.2.0
h5py                             3.9.0
holidays                         0.30
holoviews                        1.17.1
html5lib                         1.1
httpimport                       1.3.1
httplib2                         0.22.0
humanize                         4.7.0
hyperopt                         0.2.7
idna                             3.4
imageio                          2.31.1
imageio-ffmpeg                   0.4.8
imagesize                        1.4.1
imbalanced-learn                 0.10.1
imgaug                           0.4.0
importlib-metadata               6.8.0
importlib-resources              6.0.1
imutils                          0.5.4
inflect                          7.0.0
iniconfig                        2.0.0
intel-openmp                     2023.2.0
ipykernel                        5.5.6
ipython                          7.34.0
ipython-genutils                 0.2.0
ipython-sql                      0.5.0
ipywidgets                       7.7.1
itsdangerous                     2.1.2
jax                              0.4.14
jaxlib                           0.4.14+cuda11.cudnn86
jeepney                          0.7.1
jieba                            0.42.1
Jinja2                           3.1.2
joblib                           1.3.2
jsonpickle                       3.0.2
jsonschema                       4.19.0
jsonschema-specifications        2023.7.1
jupyter-client                   6.1.12
jupyter-console                  6.1.0
jupyter_core                     5.3.1
jupyter-server                   1.24.0
jupyterlab-pygments              0.2.2
jupyterlab-widgets               3.0.8
kaggle                           1.5.16
keras                            2.12.0
keyring                          23.5.0
kiwisolver                       1.4.4
langcodes                        3.3.0
launchpadlib                     1.10.16
lava                             0.4.1
lava-dl                          0.4.0
lava-nc                          0.8.0
lazr.restfulclient               0.14.4
lazr.uri                         1.0.6
lazy_loader                      0.3
libclang                         16.0.6
librosa                          0.10.1
lightgbm                         4.0.0
linecache2                       1.0.0
linkify-it-py                    2.0.2
lit                              16.0.6
llvmlite                         0.39.1
locket                           1.0.0
logical-unification              0.4.6
LunarCalendar                    0.0.9
lxml                             4.9.3
Markdown                         3.4.4
markdown-it-py                   3.0.0
MarkupSafe                       2.1.3
matplotlib                       3.7.1
matplotlib-inline                0.1.6
matplotlib-venn                  0.11.9
mdit-py-plugins                  0.4.0
mdurl                            0.1.2
miniKanren                       1.0.3
missingno                        0.5.2
mistune                          0.8.4
mizani                           0.9.2
mkl                              2023.2.0
ml-dtypes                        0.2.0
mlxtend                          0.22.0
more-itertools                   10.1.0
moviepy                          1.0.3
mpmath                           1.3.0
msgpack                          1.0.5
multidict                        6.0.4
multipledispatch                 1.0.0
multitasking                     0.0.11
murmurhash                       1.0.9
music21                          9.1.0
natsort                          8.4.0
nbclassic                        1.0.0
nbclient                         0.8.0
nbconvert                        6.5.4
nbformat                         5.9.2
nest-asyncio                     1.5.7
networkx                         2.8.7
nibabel                          4.0.2
ninja                            1.11.1
nltk                             3.8.1
norse                            1.0.0
notebook                         6.5.5
notebook_shim                    0.2.3
numba                            0.56.4
numexpr                          2.8.5
numpy                            1.25.2
nvidia-cublas-cu11               11.10.3.66
nvidia-cuda-nvrtc-cu11           11.7.99
nvidia-cuda-runtime-cu11         11.7.99
nvidia-cudnn-cu11                8.5.0.96
oauth2client                     4.1.3
oauthlib                         3.2.2
opencv-contrib-python            4.8.0.76
opencv-python                    4.8.0.76
opencv-python-headless           4.8.0.76
openpyxl                         3.1.2
opt-einsum                       3.3.0
optax                            0.1.7
orbax-checkpoint                 0.3.4
osqp                             0.6.2.post8
packaging                        23.1
pandas                           1.5.3
pandas-datareader                0.10.0
pandas-gbq                       0.17.9
pandocfilters                    1.5.0
panel                            1.2.1
param                            1.13.0
parso                            0.8.3
partd                            1.4.0
pathlib                          1.0.1
pathy                            0.10.2
patsy                            0.5.3
pexpect                          4.8.0
pickleshare                      0.7.5
Pillow                           9.4.0
pip                              23.1.2
pip-tools                        6.13.0
platformdirs                     3.10.0
plotly                           5.15.0
plotnine                         0.12.2
pluggy                           1.2.0
polars                           0.17.3
pooch                            1.7.0
portpicker                       1.5.2
prefetch-generator               1.0.3
preshed                          3.0.8
prettytable                      3.8.0
proglog                          0.1.10
progressbar2                     4.2.0
prometheus-client                0.17.1
promise                          2.3
prompt-toolkit                   3.0.39
prophet                          1.1.4
proto-plus                       1.22.3
protobuf                         3.20.3
psutil                           5.9.5
psycopg2                         2.9.7
ptyprocess                       0.7.0
py-cpuinfo                       9.0.0
py4j                             0.10.9.7
pyarrow                          9.0.0
pyasn1                           0.5.0
pyasn1-modules                   0.3.0
pycocotools                      2.0.7
pycparser                        2.21
pyct                             0.5.0
pydantic                         2.2.0
pydantic_core                    2.6.0
pydata-google-auth               1.8.2
pydot                            1.4.2
pydot-ng                         2.0.0
pydotplus                        2.0.2
PyDrive                          1.3.1
PyDrive2                         1.6.3
pyerfa                           2.0.0.3
pygame                           2.5.1
Pygments                         2.16.1
PyGObject                        3.42.1
PyJWT                            2.3.0
pymc                             5.7.2
PyMeeus                          0.5.12
pymystem3                        0.2.0
PyOpenGL                         3.1.7
pyOpenSSL                        23.2.0
pyparsing                        3.1.1
pyproj                           3.6.0
pyproject_hooks                  1.0.0
PySocks                          1.7.1
pytensor                         2.14.2
pytest                           7.4.0
python-apt                       0.0.0
python-dateutil                  2.8.2
python-louvain                   0.16
python-slugify                   8.0.1
python-utils                     3.7.0
pytz                             2023.3
pyviz_comms                      3.0.0
PyWavelets                       1.4.1
PyYAML                           6.0.1
pyzmq                            23.2.1
qdldl                            0.1.7.post0
qudida                           0.0.4
referencing                      0.30.2
regex                            2023.6.3
requests                         2.31.0
requests-oauthlib                1.3.1
requirements-parser              0.5.0
rich                             13.5.2
rpds-py                          0.9.2
rpy2                             3.4.2
rsa                              4.9
scikit-image                     0.19.3
scikit-learn                     1.2.2
scipy                            1.10.1
scs                              3.2.3
seaborn                          0.12.2
SecretStorage                    3.3.1
Send2Trash                       1.8.2
setuptools                       67.7.2
shapely                          2.0.1
six                              1.16.0
sklearn-pandas                   2.2.0
smart-open                       6.3.0
sniffio                          1.3.0
snowballstemmer                  2.2.0
sortedcontainers                 2.4.0
soundfile                        0.12.1
soupsieve                        2.4.1
soxr                             0.3.6
spacy                            3.6.1
spacy-legacy                     3.0.12
spacy-loggers                    1.0.4
Sphinx                           5.0.2
sphinxcontrib-applehelp          1.0.7
sphinxcontrib-devhelp            1.0.5
sphinxcontrib-htmlhelp           2.0.4
sphinxcontrib-jsmath             1.0.1
sphinxcontrib-qthelp             1.0.6
sphinxcontrib-serializinghtml    1.1.8
SQLAlchemy                       2.0.20
sqlparse                         0.4.4
srsly                            2.4.7
statsmodels                      0.14.0
sympy                            1.12
tables                           3.8.0
tabulate                         0.9.0
tbb                              2021.10.0
tblib                            2.0.0
tenacity                         8.2.3
tensorboard                      2.12.3
tensorboard-data-server          0.7.1
tensorflow                       2.12.0
tensorflow-datasets              4.9.2
tensorflow-estimator             2.12.0
tensorflow-gcs-config            2.12.0
tensorflow-hub                   0.14.0
tensorflow-io-gcs-filesystem     0.33.0
tensorflow-metadata              1.14.0
tensorflow-probability           0.20.1
tensorstore                      0.1.41
termcolor                        2.3.0
terminado                        0.17.1
text-unidecode                   1.3
textblob                         0.17.1
tf-slim                          1.1.0
thinc                            8.1.12
threadpoolctl                    3.2.0
tifffile                         2023.8.12
tinycss2                         1.2.1
toml                             0.10.2
tomli                            2.0.1
toolz                            0.12.0
torch                            1.13.1
torchaudio                       2.0.2+cu118
torchdata                        0.6.1
torchsummary                     1.5.1
torchtext                        0.15.2
torchvision                      0.14.1
tornado                          6.3.2
tqdm                             4.66.1
traceback2                       1.4.0
traitlets                        5.7.1
triton                           2.0.0
tweepy                           4.13.0
typer                            0.9.0
types-setuptools                 68.1.0.0
typing_extensions                4.7.1
tzlocal                          5.0.1
uc-micro-py                      1.0.2
unittest2                        1.1.0
uritemplate                      4.1.1
urllib3                          2.0.4
vega-datasets                    0.9.0
vulkan                           1.1.99.1
wadllib                          1.3.6
wasabi                           1.1.2
wcwidth                          0.2.6
webcolors                        1.13
webencodings                     0.5.1
websocket-client                 1.6.1
Werkzeug                         2.3.7
wheel                            0.41.1
widgetsnbextension               3.6.5
wordcloud                        1.9.2
wrapt                            1.14.1
xarray                           2023.7.0
xarray-einstats                  0.6.0
xgboost                          1.7.6
xlrd                             2.0.1
xyzservices                      2023.7.0
yarl                             1.9.2
yellowbrick                      1.5
yfinance                         0.2.28
zict                             3.0.0
zipp                             3.16.2

Any help would be greatly appreciated!

I saw issues #280 and #344 were relevant, but were closed because they weren't easily reproducible, hopefully this helps in fixing the bug.

Jegp commented 1 year ago

This may be caused by torch being updated, so the ABI for the compiled Norse module changes (see https://norse.github.io/norse/pages/installing.html#common-problems). Could you try to uninstall/reinstall torch, and then reinstall Norse? Re-compiling the binaries should fix the problem.

gcervantes8 commented 1 year ago

Yep! Looks like I'm able to correctly install Norse in Google Colab with the following commands:

!pip install norse
!pip install lava
!pip install lava-dl

!pip uninstall triton
!pip uninstall torchvision

!pip uninstall norse
!pip install norse
Jegp commented 1 year ago

Urgh, that seems annoyingly specific. Thank you for posting the fix!