Scikit-image

Hello,

im trying to start a training on my AGX Xavier Jetson,

I got the following error:

ImportError: /home/jetson/PycharmProjects/keypoint_rcnn_training_pytorch/venv/lib/python3.8/site-packages/sklearn/__check_build/…/…/scikit_learn.libs/libgomp-d22c30c5.so.1.0.0: cannot allocate memory in static TLS block


Contents of /home/jetson/PycharmProjects/keypoint_rcnn_training_pytorch/venv/lib/python3.8/site-packages/sklearn/__check_build:
init.py _check_build.cpython-38-aarch64-linux-gnu.sosetup.py
pycache


It seems that scikit-learn has not been built correctly.
Your install of scikit-image appears to be broken.
Try re-installing the package following the instructions at:

I read all the previous post, but none could help me.
python3 -c ‘import torch; print(torch.cuda.is_available())’ is TRUE,
so i can run on CUDA on my GPU.

im trying to import:

import os, json, numpy as np, matplotlib.pyplot as plt
import cv2
import torch
from torch.utils.data import Dataset, DataLoader
import torchvision
from torchvision.models.detection.rpn import AnchorGenerator
from torchvision.transforms import functional as F
import albumentations as A # Library for augmentations

used wheel:
pip3 install torch-1.13.0a0+340c4120.nv22.06-cp38-cp38-linux_aarch64.whl

prior to wheel install:
sudo apt-get install libopenblas-base libopenmpi-dev
sudo apt-get install libjpeg-dev zlib1g-dev libpython3-dev libavcodec-dev libavformat-dev libswscale-dev

de-installed all packages and installed again.

Anybody an idea how to continue?

Addition an overview of the packages installed:
(base) jetson@ubuntu:~/Downloads$ python -m pip freeze
absl-py==1.3.0
apturl==0.5.2
argon2-cffi==21.3.0
argon2-cffi-bindings==21.2.0
asttokens==2.0.8
astunparse==1.6.3
attrs==22.1.0
backcall==0.2.0
bcrypt==3.1.7
beautifulsoup4==4.11.1
bleach==5.0.1
blinker==1.4
Brlapi==0.7.0
cachetools==5.2.0
certifi==2019.11.28
cffi==1.15.1
chardet==3.0.4
Click==7.0
colorama==0.4.3
cryptography==2.8
cupshelpers==1.0
cycler==0.10.0
dbus-python==1.2.16
debugpy==1.6.3
decorator==4.4.2
defer==1.0.6
defusedxml==0.7.1
distro==1.4.0
distro-info===0.23ubuntu1
docker==4.3.1
duplicity==0.8.12.0
entrypoints==0.3
exceptiongroup==1.0.0
executing==1.0.0
expecttest==0.1.4
fasteners==0.14.1
fastjsonschema==2.16.2
filelock==3.8.0
future==0.18.2
google-auth==2.13.0
google-auth-oauthlib==0.4.6
graphsurgeon==0.4.6
grpcio==1.50.0
h5py==3.6.0
httplib2==0.14.0
hypothesis==6.56.4
idna==2.8
imageio==2.22.3
importlib-metadata==4.12.0
importlib-resources==5.9.0
ipykernel==6.15.3
ipython==8.5.0
ipython-genutils==0.2.0
ipywidgets==8.0.2
jedi==0.18.1
jetson-stats==3.1.4
Jetson.GPIO==2.0.20
Jinja2==3.1.2
joblib==1.1.0
jsonschema==4.16.0
jupyter==1.0.0
jupyter-console==6.4.4
jupyter-core==4.11.1
jupyter_client==7.3.5
jupyterlab-pygments==0.2.2
jupyterlab-widgets==3.0.3
keyring==18.0.1
kiwisolver==1.0.1
language-selector==0.1
launchpadlib==1.10.13
lazr.restfulclient==0.14.2
lazr.uri==1.0.3
lockfile==0.12.2
louis==3.12.0
lxml==4.9.1
macaroonbakery==1.3.1
Mako==1.1.0
Markdown==3.4.1
MarkupSafe==2.1.1
matplotlib==3.1.2
matplotlib-inline==0.1.6
mistune==2.0.4
monotonic==1.5
mpmath==1.2.1
nbclient==0.6.8
nbconvert==7.0.0
nbformat==5.6.0
nest-asyncio==1.5.5
networkx==2.8.8
notebook==6.4.12
numpy==1.23.4
nvidia-tao==0.1.24
oauthlib==3.1.0
olefile==0.46
onboard==1.4.1
packaging==21.3
pandas==0.25.3
pandocfilters==1.5.0
paramiko==2.6.0
parso==0.8.3
pbr==5.11.0
pexpect==4.6.0
pickleshare==0.7.5
Pillow==9.0.1
pkgutil_resolve_name==1.3.10
prometheus-client==0.14.1
prompt-toolkit==3.0.31
protobuf==3.6.1
psutil==5.9.2
ptyprocess==0.7.0
pure-eval==0.2.2
pyasn1==0.4.8
pyasn1-modules==0.2.8
pycairo==1.16.2
pycocotools==2.0.4
pycparser==2.21
pycrypto==2.6.1
pycups==1.9.73
Pygments==2.13.0
PyGObject==3.36.0
PyJWT==1.7.1
pymacaroons==0.13.0
PyNaCl==1.3.0
pyparsing==2.4.6
pyRFC3339==1.1
pyrsistent==0.18.1
python-apt==2.0.0+ubuntu0.20.4.8
python-dateutil==2.8.2
python-dbusmock==0.19
python-debian===0.1.36ubuntu1
pytz==2019.3
PyWavelets==1.4.1
pyxattr==0.6.1
pyxdg==0.26
PyYAML==5.3.1
pyzmq==24.0.1
qtconsole==5.3.2
QtPy==2.2.0
requests==2.22.0
requests-oauthlib==1.3.1
requests-unixsocket==0.2.0
rsa==4.9
scikit-build==0.15.0
scikit-image==0.19.3
scikit-learn==1.1.3
scipy==1.8.0
SecretStorage==2.3.1
Send2Trash==1.8.0
simplejson==3.16.0
six==1.14.0
sortedcontainers==2.4.0
soupsieve==2.3.2.post1
stack-data==0.5.0
sympy==1.11.1
systemd-python==234
tabulate==0.8.10
tensorboard==2.10.1
tensorboard-data-server==0.6.1
tensorboard-plugin-wit==1.8.1
tensorrt==8.4.1.5
terminado==0.15.0
testresources==2.0.1
threadpoolctl==3.1.0
tifffile==2022.10.10
tinycss2==1.1.1
torchvision==0.13.0
tornado==6.2
traitlets==5.4.0
types-dataclasses==0.6.6
typing_extensions==4.4.0
ubuntu-advantage-tools==27.11.2
ubuntu-drivers-common==0.0.0
uff==0.6.9
urllib3==1.25.8
urwid==2.0.1
wadllib==1.3.3
wcwidth==0.2.5
webencodings==0.5.1
websocket-client==1.4.1
Werkzeug==2.2.2
widgetsnbextension==4.0.3
xkit==0.0.0
youtube-dl==2020.3.24
zipp==3.8.1
(base) jetson@ubuntu:~/Downloads$ python -c “import sklearn; sklearn.show_versions()”

System:
python: 3.8.10 (default, Jun 22 2022, 20:18:18) [GCC 9.4.0]
executable: /usr/bin/python3
machine: Linux-5.10.104-tegra-aarch64-with-glibc2.29

Python dependencies:
sklearn: 1.1.3
pip: 22.3
setuptools: 58.3.0
numpy: 1.23.4
scipy: 1.8.0
Cython: None
pandas: 0.25.3
matplotlib: 3.1.2
joblib: 1.1.0
threadpoolctl: 3.1.0

Built with OpenMP: True

threadpoolctl info:
user_api: openmp
internal_api: openmp
prefix: libgomp
filepath: /usr/lib/aarch64-linux-gnu/libgomp.so.1.0.0
version: None
num_threads: 8

   user_api: openmp

internal_api: openmp
prefix: libgomp
filepath: /usr/local/lib/python3.8/dist-packages/scikit_learn.libs/libgomp-d22c30c5.so.1.0.0
version: None
num_threads: 8

   user_api: blas

internal_api: openblas
prefix: libopenblas
filepath: /home/jetson/.local/lib/python3.8/site-packages/numpy.libs/libopenblas64_p-r0-9c1f2efe.3.20.so
version: 0.3.20
threading_layer: pthreads
architecture: armv8
num_threads: 8

   user_api: blas

internal_api: openblas
prefix: libopenblas
filepath: /home/jetson/.local/lib/python3.8/site-packages/scipy.libs/libopenblasp-r0-444d0ba0.3.17.so
version: 0.3.17
threading_layer: pthreads
architecture: armv8
num_threads: 8
(base) jetson@ubuntu:~/Downloads$

There is no update from you for a period, assuming this is not an issue any more.
Hence we are closing this topic. If need further support, please open a new one.
Thanks

Hi,

We don’t preinstall scikit-image with JetPack. Are you using NGC docker?
If yes, could you please share which container you use?

Thanks.

This topic was automatically closed 14 days after the last reply. New replies are no longer allowed.