search

zudi-lin / pytorch_connectomics

PyTorch Connectomics: segmentation toolbox for EM connectomics
http://connectomics.readthedocs.io/
MIT License
169 stars 77 forks source link

Issue with installing waterz used for neuron segmentation tutorial #141

Closed PG-Gu closed 4 months ago

PG-Gu commented 5 months ago

Dear developers,

Hello! I'm trying to run the experiment in neuron segmentation tutorial However I was stuck in the "Get segmentation" section since I met issues with the waterz package. I'm using Ubuntu 22.04.2 LTS and Python 2.7.18 I succesfully installed the waterz package following the instruction but it reported following error: waterz at thresholds [0.1, 0.3, 0.6] Compiling waterz in /home/wenqi/.cython/inline Traceback (most recent call last): File "snemi_test_seg.py", line 29, in <module> aff_threshold=aff_thresholds, gt=seg_gt) File "/home/wenqi/miniconda2/envs/waterz/lib/python2.7/site-packages/waterz-0.8-py2.7-linux-x86_64.egg/waterz/seg_waterz.py", line 56, in waterz force_rebuild=True)): File "/home/wenqi/miniconda2/envs/waterz/lib/python2.7/site-packages/waterz-0.8-py2.7-linux-x86_64.egg/waterz/__init__.py", line 250, in agglomerate return __import__(module_name).agglomerate( ImportError: /home/wenqi/.cython/inline/waterz_bd99d59b2f8e1db6a4d70afd4da36e04.so: undefined symbol: _ZSt28__throw_bad_array_new_lengthv

I wonder if you have any ideas regarding what caused this problem? Thanks in advance!

donglaiw commented 4 months ago

need to change the gcc version: https://github.com/stan-dev/pystan/issues/294