search

isl-org / Open3D-ML

An extension of Open3D to address 3D Machine Learning tasks
Other
1.87k stars 321 forks source link

Impossible to run on Ubuntu Segmentation fault (core dumped) #660

Closed francescobodria closed 1 month ago

francescobodria commented 1 month ago

Checklist

Steps to reproduce the issue

I first cloned Open3D-ML by:

git clone https://github.com/isl-org/Open3D-ML.git
cd Open3D-ML

Then, I set OPEN3D_ML_ROOT with:

source set_open3d_ml_root.sh

Built the enviroment

conda create -n open3d-ml python=3.11
git checkout v0.18.0 
pip install requirements-torch-cuda.txt
pip install requirements.txt
pip install open3d

Then I runned the tensorboad_pytorch.py in the example folder

cd examples
python tensorboard_pytorch.py
tensorboard --logdir demo_logs/pytorch

Error message

TensorFlow installation not found - running with reduced feature set.
Using external Open3D-ML in /innovation/Open3D-ML

NOTE: Using experimental fast data loading logic. To disable, pass
    "--load_fast=false" and report issues on GitHub. More details:
    https://github.com/tensorflow/tensorboard/issues/4784

TensorBoard 2.18.0 at http://0.0.0.0:13000/ (Press CTRL+C to quit)
[Open3D INFO] WebRTCWindowSystem: HTTP handshake server disabled.
[Open3D INFO] WebRTC GUI backend enabled.
[Open3D INFO] Resetting default logger to print to terminal.
[Open3D INFO] Window window_0 created.
[Open3D INFO] EGL headless mode enabled.
[Open3D INFO] ICE servers: ["stun:stun.l.google.com:19302", "turn:user:password@34.69.27.100:3478", "turn:user:password@34.69.27.100:3478?transport=tcp"]
FEngine (64 bits) created at 0x7f118800a040 (threading is enabled)
[Open3D INFO] Set WEBRTC_STUN_SERVER environment variable add a customized WebRTC STUN server.
[Open3D INFO] WebRTC Jupyter handshake mode enabled.
EGL(1.5)
OpenGL(4.1)
[Open3D INFO] Window window_1 created.
Fatal Python error: Segmentation fault

Current thread 0x00007f1193fff700 (most recent call first):
  File "/anaconda/envs/open3d-ml/lib/python3.11/site-packages/open3d/visualization/tensorboard_plugin/plugin.py", line 397 in _create_ui
  File "/anaconda/envs/open3d-ml/lib/python3.11/site-packages/open3d/visualization/async_event_loop.py", line 79 in _thread_main
  File "/anaconda/envs/open3d-ml/lib/python3.11/threading.py", line 975 in run
  File "/anaconda/envs/open3d-ml/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/anaconda/envs/open3d-ml/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f11b1ffb700 (most recent call first):
  File "/anaconda/envs/open3d-ml/lib/python3.11/threading.py", line 320 in wait
  File "/anaconda/envs/open3d-ml/lib/python3.11/threading.py", line 355 in wait_for
  File "/anaconda/envs/open3d-ml/lib/python3.11/site-packages/open3d/visualization/async_event_loop.py", line 64 in run_sync
  File "/anaconda/envs/open3d-ml/lib/python3.11/site-packages/open3d/visualization/tensorboard_plugin/plugin.py", line 65 in __init__
  File "/anaconda/envs/open3d-ml/lib/python3.11/site-packages/open3d/visualization/tensorboard_plugin/plugin.py", line 696 in _new_window
  File "/anaconda/envs/open3d-ml/lib/python3.11/site-packages/werkzeug/wrappers/request.py", line 190 in application
  File "/anaconda/envs/open3d-ml/lib/python3.11/site-packages/tensorboard/backend/application.py", line 551 in _route_request
  File "/anaconda/envs/open3d-ml/lib/python3.11/site-packages/tensorboard/backend/auth_context_middleware.py", line 38 in __call__
  File "/anaconda/envs/open3d-ml/lib/python3.11/site-packages/tensorboard/backend/client_feature_flags.py", line 55 in __call__
  File "/anaconda/envs/open3d-ml/lib/python3.11/site-packages/tensorboard/backend/empty_path_redirect.py", line 43 in __call__
  File "/anaconda/envs/open3d-ml/lib/python3.11/site-packages/tensorboard/backend/experiment_id.py", line 73 in __call__
  File "/anaconda/envs/open3d-ml/lib/python3.11/site-packages/tensorboard/backend/path_prefix.py", line 68 in __call__
  File "/anaconda/envs/open3d-ml/lib/python3.11/site-packages/tensorboard/backend/security_validator.py", line 91 in __call__
  File "/anaconda/envs/open3d-ml/lib/python3.11/site-packages/tensorboard/backend/application.py", line 569 in wrapper
  File "/anaconda/envs/open3d-ml/lib/python3.11/site-packages/tensorboard/backend/application.py", line 528 in __call__
  File "/anaconda/envs/open3d-ml/lib/python3.11/site-packages/werkzeug/serving.py", line 331 in execute
  File "/anaconda/envs/open3d-ml/lib/python3.11/site-packages/werkzeug/serving.py", line 370 in run_wsgi
  File "/anaconda/envs/open3d-ml/lib/python3.11/http/server.py", line 419 in handle_one_request
  File "/anaconda/envs/open3d-ml/lib/python3.11/http/server.py", line 431 in handle
  File "/anaconda/envs/open3d-ml/lib/python3.11/site-packages/werkzeug/serving.py", line 398 in handle
  File "/anaconda/envs/open3d-ml/lib/python3.11/socketserver.py", line 755 in __init__
  File "/anaconda/envs/open3d-ml/lib/python3.11/socketserver.py", line 361 in finish_request
  File "/anaconda/envs/open3d-ml/lib/python3.11/socketserver.py", line 691 in process_request_thread
  File "/anaconda/envs/open3d-ml/lib/python3.11/threading.py", line 975 in run
  File "/anaconda/envs/open3d-ml/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/anaconda/envs/open3d-ml/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f1240b25740 (most recent call first):
  File "/anaconda/envs/open3d-ml/lib/python3.11/selectors.py", line 415 in select
  File "/anaconda/envs/open3d-ml/lib/python3.11/socketserver.py", line 233 in serve_forever
  File "/anaconda/envs/open3d-ml/lib/python3.11/site-packages/werkzeug/serving.py", line 817 in serve_forever
  File "/anaconda/envs/open3d-ml/lib/python3.11/site-packages/tensorboard/program.py", line 297 in _run_serve_subcommand
  File "/anaconda/envs/open3d-ml/lib/python3.11/site-packages/tensorboard/program.py", line 278 in main
  File "/anaconda/envs/open3d-ml/lib/python3.11/site-packages/absl/app.py", line 254 in _run_main
  File "/anaconda/envs/open3d-ml/lib/python3.11/site-packages/absl/app.py", line 308 in run
  File "/anaconda/envs/open3d-ml/lib/python3.11/site-packages/tensorboard/main.py", line 41 in run_main
  File "/anaconda/envs/open3d-ml/bin/tensorboard", line 8 in <module>

Extension modules: markupsafe._speedups, google._upb._message, numpy._core._multiarray_umath, numpy.linalg._umath_linalg, grpc._cython.cygrpc, sklearn.__check_build._check_build, scipy._lib._ccallback_c, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, charset_normalizer.md, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation, scipy.optimize._group_columns, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.optimize._direct, scipy.integrate._odepack, scipy.integrate._quadpack, scipy.integrate._vode, scipy.integrate._dop, scipy.integrate._lsoda, scipy.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, scipy.special.cython_special, scipy.stats._stats, scipy.stats._biasedurn, scipy.stats._levy_stable.levyst, scipy.stats._stats_pythran, scipy._lib._uarray._uarray, scipy.stats._ansari_swilk_statistics, scipy.stats._sobol, scipy.stats._qmc_cy, scipy.stats._mvn, scipy.stats._rcont.rcont, scipy.stats._unuran.unuran_wrapper, scipy.ndimage._nd_image, _ni_label, scipy.ndimage._ni_label, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.strptime, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.lib, pandas._libs.ops, pandas._libs.hashing, pandas._libs.arrays, pandas._libs.tslib, pandas._libs.sparse, pandas._libs.internals, pandas._libs.indexing, pandas._libs.index, pandas._libs.writers, pandas._libs.join, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.json, pandas._libs.parsers, pandas._libs.testing, sklearn.utils._isfinite, sklearn.utils.sparsefuncs_fast, sklearn.utils.murmurhash, sklearn.utils._openmp_helpers, sklearn.metrics.cluster._expected_mutual_info_fast, sklearn.preprocessing._csr_polynomial_expansion, sklearn.preprocessing._target_encoder_fast, sklearn.metrics._dist_metrics, sklearn.metrics._pairwise_distances_reduction._datasets_pair, sklearn.utils._cython_blas, sklearn.metrics._pairwise_distances_reduction._base, sklearn.metrics._pairwise_distances_reduction._middle_term_computer, sklearn.utils._heap, sklearn.utils._sorting, sklearn.metrics._pairwise_distances_reduction._argkmin, sklearn.metrics._pairwise_distances_reduction._argkmin_classmode, sklearn.utils._vector_sentinel, sklearn.metrics._pairwise_distances_reduction._radius_neighbors, sklearn.metrics._pairwise_distances_reduction._radius_neighbors_classmode, sklearn.metrics._pairwise_fast, sklearn.neighbors._partition_nodes, sklearn.neighbors._ball_tree, sklearn.neighbors._kd_tree, sklearn.utils.arrayfuncs, sklearn.utils._random, sklearn.utils._seq_dataset, sklearn.linear_model._cd_fast, _loss, sklearn._loss._loss, sklearn.svm._liblinear, sklearn.svm._libsvm, sklearn.svm._libsvm_sparse, sklearn.utils._weight_vector, sklearn.linear_model._sgd_fast, sklearn.linear_model._sag_fast, sklearn.decomposition._online_lda_fast, sklearn.decomposition._cdnmf_fast, yaml._yaml, PIL._imaging (total: 179)
Segmentation fault (core dumped)

Open3D, Python and System information

- Operating system: Ubuntu 20.04.6 LTS
- Python version: python 3.11
- Open3D version: v0.18.0
- System type: x84
- Is this remote workstation?: yes
- How did you install Open3D?: pip
- Compiler version (if built from source): gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0

Additional information

The script worked and create the subfolders in the example folder But when I open a tensorboard page it did not load the GUI and the terminal gives me the segmentation fault error What am I doing wrong?

francescobodria commented 1 month ago

I found the problem: it was the numpy version I downgraded to version 1.26.4 and everything is working now