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kedro-org / kedro

Kedro is a toolbox for production-ready data science. It uses software engineering best practices to help you create data engineering and data science pipelines that are reproducible, maintainable, and modular.
https://kedro.org
Apache License 2.0
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Segmentation fault after issuing `kedro install` #169

Closed anferico closed 4 years ago

anferico commented 4 years ago

Description

I was following this tutorial to create a new project using Kedro, however I get a Segmentation fault error after I run kedro install.

Context

My goal was to follow the tutorial and create an example project to explore Kedro's functionalities.

Steps to Reproduce

Here's what I did exactly:

  1. pip3 install kedro
  2. mkdir kedro_example_project && cd kedro_example_project
  3. kedro new, following the instructions. The project's root directory is kedro-tutorial
  4. virtualenv -p /usr/bin/python3 .venv
  5. source .venv/bin/activate, thus activating the virtual environment
  6. cd kedro-tutorial
  7. kedro install

Expected Result

Project dependencies are correctly installed

Actual Result

Project dependencies claimed to be correctly installed (Successfully installed ...), but then pip outputs an additional line of text: Segmentation fault. If I try to run pip freeze from within the virtual environment, I notice that such dependencies were not installed

Full output of kedro install:

/usr/bin/python3 -m pip install -U -r src/requirements.txt
Collecting ipython<8.0,>=7.0.0 (from -r src/requirements.txt (line 1))
  Cache entry deserialization failed, entry ignored
  Using cached https://files.pythonhosted.org/packages/81/2e/59cdacea6476a4c21b7c090a91250ffbcd085900f5eb9f4e4d68dd2ee4e3/ipython-7.9.0-py3-none-any.whl
Collecting jupyter<2.0,>=1.0.0 (from -r src/requirements.txt (line 2))
  Cache entry deserialization failed, entry ignored
  Using cached https://files.pythonhosted.org/packages/83/df/0f5dd132200728a86190397e1ea87cd76244e42d39ec5e88efd25b2abd7e/jupyter-1.0.0-py2.py3-none-any.whl
Collecting jupyter_client<6.0,>=5.1.0 (from -r src/requirements.txt (line 3))
  Cache entry deserialization failed, entry ignored
  Using cached https://files.pythonhosted.org/packages/13/81/fe0eee1bcf949851a120254b1f530ae1e01bdde2d3ab9710c6ff81525061/jupyter_client-5.3.4-py2.py3-none-any.whl
Collecting jupyterlab==0.31.1 (from -r src/requirements.txt (line 4))
  Cache entry deserialization failed, entry ignored
  Using cached https://files.pythonhosted.org/packages/73/e9/1160ac156eb435430a7419c0b9134b13c7cbf04589b083fc9d22e52cdd74/jupyterlab-0.31.1-py2.py3-none-any.whl
Collecting kedro==0.15.4 (from -r src/requirements.txt (line 5))
  Cache entry deserialization failed, entry ignored
  Using cached https://files.pythonhosted.org/packages/68/19/1f374fbc42b1b13db3f033d9b750474b80de3a294648e0f1c425d730b036/kedro-0.15.4-py3-none-any.whl
Collecting nbstripout==0.3.3 (from -r src/requirements.txt (line 6))
  Cache entry deserialization failed, entry ignored
  Using cached https://files.pythonhosted.org/packages/1c/37/2de0322bffacece7f4519486287020a00c0f9887a45c46e43606193b05fb/nbstripout-0.3.3-py2.py3-none-any.whl
Collecting pytest-cov<3.0,>=2.5 (from -r src/requirements.txt (line 7))
  Cache entry deserialization failed, entry ignored
  Using cached https://files.pythonhosted.org/packages/b9/54/3673ee8be482f81527678ac894276223b9814bb7262e4f730469bb7bf70e/pytest_cov-2.8.1-py2.py3-none-any.whl
Collecting pytest-mock<2.0,>=1.7.1 (from -r src/requirements.txt (line 8))
  Cache entry deserialization failed, entry ignored
  Using cached https://files.pythonhosted.org/packages/5c/d8/dc124532a6b5b42ea817f00097d8c9b9bbd3d49f1a2e6f7648f057a8e191/pytest_mock-1.12.1-py2.py3-none-any.whl
Collecting pytest<4.0,>=3.4 (from -r src/requirements.txt (line 9))
  Cache entry deserialization failed, entry ignored
  Using cached https://files.pythonhosted.org/packages/57/94/305477fb977546970a3464c21b63c6800df6705384af2978b89acccfb151/pytest-3.10.1-py2.py3-none-any.whl
Collecting wheel==0.32.2 (from -r src/requirements.txt (line 10))
  Using cached https://files.pythonhosted.org/packages/5a/9b/6aebe9e2636d35d1a93772fa644c828303e1d5d124e8a88f156f42ac4b87/wheel-0.32.2-py2.py3-none-any.whl
Collecting traitlets>=4.2 (from ipython<8.0,>=7.0.0->-r src/requirements.txt (line 1))
  Using cached https://files.pythonhosted.org/packages/ca/ab/872a23e29cec3cf2594af7e857f18b687ad21039c1f9b922fac5b9b142d5/traitlets-4.3.3-py2.py3-none-any.whl
Collecting decorator (from ipython<8.0,>=7.0.0->-r src/requirements.txt (line 1))
  Using cached https://files.pythonhosted.org/packages/8f/b7/f329cfdc75f3d28d12c65980e4469e2fa373f1953f5df6e370e84ea2e875/decorator-4.4.1-py2.py3-none-any.whl
Collecting prompt-toolkit<2.1.0,>=2.0.0 (from ipython<8.0,>=7.0.0->-r src/requirements.txt (line 1))
  Using cached https://files.pythonhosted.org/packages/87/61/2dfea88583d5454e3a64f9308a686071d58d59a55db638268a6413e1eb6d/prompt_toolkit-2.0.10-py3-none-any.whl
Collecting setuptools>=18.5 (from ipython<8.0,>=7.0.0->-r src/requirements.txt (line 1))
  Using cached https://files.pythonhosted.org/packages/d9/de/554b6310ac87c5b921bc45634b07b11394fe63bc4cb5176f5240addf18ab/setuptools-41.6.0-py2.py3-none-any.whl
Collecting pickleshare (from ipython<8.0,>=7.0.0->-r src/requirements.txt (line 1))
  Using cached https://files.pythonhosted.org/packages/9a/41/220f49aaea88bc6fa6cba8d05ecf24676326156c23b991e80b3f2fc24c77/pickleshare-0.7.5-py2.py3-none-any.whl
Collecting pygments (from ipython<8.0,>=7.0.0->-r src/requirements.txt (line 1))
  Using cached https://files.pythonhosted.org/packages/5c/73/1dfa428150e3ccb0fa3e68db406e5be48698f2a979ccbcec795f28f44048/Pygments-2.4.2-py2.py3-none-any.whl
Collecting pexpect; sys_platform != "win32" (from ipython<8.0,>=7.0.0->-r src/requirements.txt (line 1))
  Using cached https://files.pythonhosted.org/packages/0e/3e/377007e3f36ec42f1b84ec322ee12141a9e10d808312e5738f52f80a232c/pexpect-4.7.0-py2.py3-none-any.whl
Collecting jedi>=0.10 (from ipython<8.0,>=7.0.0->-r src/requirements.txt (line 1))
  Using cached https://files.pythonhosted.org/packages/55/54/da994f359e4e7da4776a200e76dbc85ba5fc319eefc22e33d55296d95a1d/jedi-0.15.1-py2.py3-none-any.whl
Collecting backcall (from ipython<8.0,>=7.0.0->-r src/requirements.txt (line 1))
Collecting ipykernel (from jupyter<2.0,>=1.0.0->-r src/requirements.txt (line 2))
  Using cached https://files.pythonhosted.org/packages/e1/92/8fec943b5b81078399f969f00557804d884c96fcd0bc296e81a2ed4fd270/ipykernel-5.1.3-py3-none-any.whl
Collecting jupyter-console (from jupyter<2.0,>=1.0.0->-r src/requirements.txt (line 2))
  Using cached https://files.pythonhosted.org/packages/cb/ee/6374ae8c21b7d0847f9c3722dcdfac986b8e54fa9ad9ea66e1eb6320d2b8/jupyter_console-6.0.0-py2.py3-none-any.whl
Collecting nbconvert (from jupyter<2.0,>=1.0.0->-r src/requirements.txt (line 2))
  Using cached https://files.pythonhosted.org/packages/79/6c/05a569e9f703d18aacb89b7ad6075b404e8a4afde2c26b73ca77bb644b14/nbconvert-5.6.1-py2.py3-none-any.whl
Collecting qtconsole (from jupyter<2.0,>=1.0.0->-r src/requirements.txt (line 2))
  Using cached https://files.pythonhosted.org/packages/7c/57/3528b84ffa753e2089908bbf74bb5ae60653eb7a63797b6234e88b847d67/qtconsole-4.6.0-py2.py3-none-any.whl
Collecting ipywidgets (from jupyter<2.0,>=1.0.0->-r src/requirements.txt (line 2))
  Using cached https://files.pythonhosted.org/packages/56/a0/dbcf5881bb2f51e8db678211907f16ea0a182b232c591a6d6f276985ca95/ipywidgets-7.5.1-py2.py3-none-any.whl
Collecting notebook (from jupyter<2.0,>=1.0.0->-r src/requirements.txt (line 2))
  Using cached https://files.pythonhosted.org/packages/f5/69/d2ffaf7efc20ce47469187e3a41e6e03e17b45de5a6559f4e7ab3eace5e1/notebook-6.0.2-py3-none-any.whl
Collecting python-dateutil>=2.1 (from jupyter_client<6.0,>=5.1.0->-r src/requirements.txt (line 3))
  Using cached https://files.pythonhosted.org/packages/d4/70/d60450c3dd48ef87586924207ae8907090de0b306af2bce5d134d78615cb/python_dateutil-2.8.1-py2.py3-none-any.whl
Collecting tornado>=4.1 (from jupyter_client<6.0,>=5.1.0->-r src/requirements.txt (line 3))
Collecting pyzmq>=13 (from jupyter_client<6.0,>=5.1.0->-r src/requirements.txt (line 3))
  Using cached https://files.pythonhosted.org/packages/94/07/cee3d328a2e13f9de1c2b62cced7a389b61ac81424f2e377f3dc9d668282/pyzmq-18.1.1-cp36-cp36m-manylinux1_x86_64.whl
Collecting jupyter-core>=4.6.0 (from jupyter_client<6.0,>=5.1.0->-r src/requirements.txt (line 3))
  Using cached https://files.pythonhosted.org/packages/fb/82/86437f661875e30682e99d04c13ba6c216f86f5f6ca6ef212d3ee8b6ca11/jupyter_core-4.6.1-py2.py3-none-any.whl
Collecting jupyterlab-launcher<0.11.0,>=0.10.0 (from jupyterlab==0.31.1->-r src/requirements.txt (line 4))
  Using cached https://files.pythonhosted.org/packages/2f/46/105843eae616cce38ea95a2ddf9cdd598bc7696d474d98e89a89d9052a10/jupyterlab_launcher-0.10.5-py2.py3-none-any.whl
Collecting ipython-genutils (from jupyterlab==0.31.1->-r src/requirements.txt (line 4))
  Using cached https://files.pythonhosted.org/packages/fa/bc/9bd3b5c2b4774d5f33b2d544f1460be9df7df2fe42f352135381c347c69a/ipython_genutils-0.2.0-py2.py3-none-any.whl
Collecting pandas<1.0,>=0.23.0 (from kedro==0.15.4->-r src/requirements.txt (line 5))
  Using cached https://files.pythonhosted.org/packages/52/3f/f6a428599e0d4497e1595030965b5ba455fd8ade6e977e3c819973c4b41d/pandas-0.25.3-cp36-cp36m-manylinux1_x86_64.whl
Collecting pip-tools<5.0.0,>=4.0.0 (from kedro==0.15.4->-r src/requirements.txt (line 5))
  Using cached https://files.pythonhosted.org/packages/53/aa/d0a0ae1e73eae5662be9df49468f1124f7f3229368a40619ab69eeb54f35/pip_tools-4.2.0-py2.py3-none-any.whl
Collecting requests<3.0,>=2.20.0 (from kedro==0.15.4->-r src/requirements.txt (line 5))
  Using cached https://files.pythonhosted.org/packages/51/bd/23c926cd341ea6b7dd0b2a00aba99ae0f828be89d72b2190f27c11d4b7fb/requests-2.22.0-py2.py3-none-any.whl
Collecting anyconfig<1.0,>=0.9.7 (from kedro==0.15.4->-r src/requirements.txt (line 5))
Collecting toposort<2.0,>=1.5 (from kedro==0.15.4->-r src/requirements.txt (line 5))
  Using cached https://files.pythonhosted.org/packages/e9/8a/321cd8ea5f4a22a06e3ba30ef31ec33bea11a3443eeb1d89807640ee6ed4/toposort-1.5-py2.py3-none-any.whl
Collecting memory-profiler<1.0,>=0.50.0 (from kedro==0.15.4->-r src/requirements.txt (line 5))
Collecting click<8.0 (from kedro==0.15.4->-r src/requirements.txt (line 5))
  Using cached https://files.pythonhosted.org/packages/fa/37/45185cb5abbc30d7257104c434fe0b07e5a195a6847506c074527aa599ec/Click-7.0-py2.py3-none-any.whl
Collecting xlsxwriter<2.0,>=1.0.0 (from kedro==0.15.4->-r src/requirements.txt (line 5))
  Using cached https://files.pythonhosted.org/packages/f2/16/da654cfbc0b05f2ad253c0f244b0c2a76c403bb774717b39c92653acb290/XlsxWriter-1.2.6-py2.py3-none-any.whl
Collecting s3fs<1.0,>=0.3.0 (from kedro==0.15.4->-r src/requirements.txt (line 5))
  Using cached https://files.pythonhosted.org/packages/72/5c/ec84c7ec49fde2c3b0d885ecae4504fa40fc77fef7684e9f2939c50f9b94/s3fs-0.4.0-py3-none-any.whl
Collecting tables<3.6,>=3.4.4 (from kedro==0.15.4->-r src/requirements.txt (line 5))
  Using cached https://files.pythonhosted.org/packages/87/f7/bb0ec32a3f3dd74143a3108fbf737e6dcfd47f0ffd61b52af7106ab7a38a/tables-3.5.2-cp36-cp36m-manylinux1_x86_64.whl
Collecting pyarrow<1.0.0,>=0.12.0 (from kedro==0.15.4->-r src/requirements.txt (line 5))
  Using cached https://files.pythonhosted.org/packages/dd/77/5865b367a6792da2f811ae49391c1f85c29b29663555aac0a118fe8e153e/pyarrow-0.15.1-cp36-cp36m-manylinux1_x86_64.whl
Collecting cookiecutter<2.0,>=1.6.0 (from kedro==0.15.4->-r src/requirements.txt (line 5))
  Using cached https://files.pythonhosted.org/packages/16/99/1ca3a75978270288354f419e9166666801cf7e7d8df984de44a7d5d8b8d0/cookiecutter-1.6.0-py2.py3-none-any.whl
Collecting xlrd<2.0,>=1.0.0 (from kedro==0.15.4->-r src/requirements.txt (line 5))
  Using cached https://files.pythonhosted.org/packages/b0/16/63576a1a001752e34bf8ea62e367997530dc553b689356b9879339cf45a4/xlrd-1.2.0-py2.py3-none-any.whl
Collecting SQLAlchemy<2.0,>=1.2.0 (from kedro==0.15.4->-r src/requirements.txt (line 5))
Collecting PyYAML<6.0,>=4.2 (from kedro==0.15.4->-r src/requirements.txt (line 5))
Collecting python-json-logger<1.0,>=0.1.9 (from kedro==0.15.4->-r src/requirements.txt (line 5))
Collecting nbformat (from nbstripout==0.3.3->-r src/requirements.txt (line 6))
  Using cached https://files.pythonhosted.org/packages/da/27/9a654d2b6cc1eaa517d1c5a4405166c7f6d72f04f6e7eea41855fe808a46/nbformat-4.4.0-py2.py3-none-any.whl
Collecting coverage>=4.4 (from pytest-cov<3.0,>=2.5->-r src/requirements.txt (line 7))
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Collecting py>=1.5.0 (from pytest<4.0,>=3.4->-r src/requirements.txt (line 9))
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Collecting more-itertools>=4.0.0 (from pytest<4.0,>=3.4->-r src/requirements.txt (line 9))
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Collecting six>=1.10.0 (from pytest<4.0,>=3.4->-r src/requirements.txt (line 9))
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Collecting attrs>=17.4.0 (from pytest<4.0,>=3.4->-r src/requirements.txt (line 9))
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Collecting atomicwrites>=1.0 (from pytest<4.0,>=3.4->-r src/requirements.txt (line 9))
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Collecting pluggy>=0.7 (from pytest<4.0,>=3.4->-r src/requirements.txt (line 9))
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Collecting pandocfilters>=1.4.1 (from nbconvert->jupyter<2.0,>=1.0.0->-r src/requirements.txt (line 2))
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Installing collected packages: ipython-genutils, decorator, six, traitlets, wcwidth, prompt-toolkit, setuptools, pickleshare, pygments, ptyprocess, pexpect, parso, jedi, backcall, ipython, python-dateutil, tornado, pyzmq, jupyter-core, jupyter-client, ipykernel, jupyter-console, entrypoints, defusedxml, testpath, MarkupSafe, jinja2, pyrsistent, more-itertools, zipp, importlib-metadata, attrs, jsonschema, nbformat, mistune, webencodings, bleach, pandocfilters, nbconvert, qtconsole, Send2Trash, terminado, prometheus-client, notebook, widgetsnbextension, ipywidgets, jupyter, jupyterlab-launcher, jupyterlab, numpy, pytz, pandas, click, pip-tools, certifi, idna, chardet, urllib3, requests, anyconfig, toposort, psutil, memory-profiler, xlsxwriter, fsspec, jmespath, docutils, botocore, s3transfer, boto3, s3fs, numexpr, mock, tables, pyarrow, whichcraft, arrow, jinja2-time, future, binaryornot, poyo, cookiecutter, xlrd, SQLAlchemy, PyYAML, python-json-logger, kedro, nbstripout, coverage, py, atomicwrites, pluggy, pytest, pytest-cov, pytest-mock, wheel
Successfully installed MarkupSafe-1.1.1 PyYAML-5.1.2 SQLAlchemy-1.3.11 Send2Trash-1.5.0 anyconfig-0.9.10 arrow-0.15.4 atomicwrites-1.3.0 attrs-19.3.0 backcall-0.1.0 binaryornot-0.4.4 bleach-3.1.0 boto3-1.10.25 botocore-1.13.25 certifi-2019.9.11 chardet-3.0.4 click-7.0 cookiecutter-1.6.0 coverage-4.5.4 decorator-4.4.1 defusedxml-0.6.0 docutils-0.15.2 entrypoints-0.3 fsspec-0.6.0 future-0.18.2 idna-2.8 importlib-metadata-0.23 ipykernel-5.1.3 ipython-7.9.0 ipython-genutils-0.2.0 ipywidgets-7.5.1 jedi-0.15.1 jinja2-2.10.3 jinja2-time-0.2.0 jmespath-0.9.4 jsonschema-3.2.0 jupyter-1.0.0 jupyter-client-5.3.4 jupyter-console-6.0.0 jupyter-core-4.6.1 jupyterlab-0.31.1 jupyterlab-launcher-0.10.5 kedro-0.15.4 memory-profiler-0.55.0 mistune-0.8.4 mock-3.0.5 more-itertools-7.2.0 nbconvert-5.6.1 nbformat-4.4.0 nbstripout-0.3.3 notebook-6.0.2 numexpr-2.7.0 numpy-1.17.4 pandas-0.25.3 pandocfilters-1.4.2 parso-0.5.1 pexpect-4.7.0 pickleshare-0.7.5 pip-tools-4.2.0 pluggy-0.13.1 poyo-0.5.0 prometheus-client-0.7.1 prompt-toolkit-2.0.10 psutil-5.6.5 ptyprocess-0.6.0 py-1.8.0 pyarrow-0.15.1 pygments-2.4.2 pyrsistent-0.15.5 pytest-3.10.1 pytest-cov-2.8.1 pytest-mock-1.12.1 python-dateutil-2.8.1 python-json-logger-0.1.11 pytz-2019.3 pyzmq-18.1.1 qtconsole-4.6.0 requests-2.22.0 s3fs-0.4.0 s3transfer-0.2.1 setuptools-41.6.0 six-1.13.0 tables-3.5.2 terminado-0.8.3 testpath-0.4.4 toposort-1.5 tornado-6.0.3 traitlets-4.3.3 urllib3-1.25.7 wcwidth-0.1.7 webencodings-0.5.1 wheel-0.32.3 whichcraft-0.6.1 widgetsnbextension-3.5.1 xlrd-1.2.0 xlsxwriter-1.2.6 zipp-0.6.0
Segmentation fault

Output of kedro info:

 _            _
| | _____  __| |_ __ ___
| |/ / _ \/ _` | '__/ _ \
|   <  __/ (_| | | | (_) |
|_|\_\___|\__,_|_|  \___/
v0.15.4

kedro allows teams to create analytics
projects. It is developed as part of
the Kedro initiative at QuantumBlack.

No plugins installed

Output of pip freeze after running kedro install:

pkg-resources==0.0.0

Your Environment

Include as many relevant details about the environment in which you experienced the bug:

tolomea commented 4 years ago

could you please include the full output, also could you please run "kedro info" and include the full output of that as well

anferico commented 4 years ago

@tolomea I've just edited my post

Flid commented 4 years ago

That looks weird. And it's likely to be caused by some specific setup on your machine, low memory or even corrupted memory. Can you please enable core dumps (something like that) and re-run the failing part? it will generate a dump file, which might give a clue what causes it.

lorenabalan commented 4 years ago

@anferico any luck following @Flid 's recommendation?

anferico commented 4 years ago

@lorenabalan Actually I solved the problem by installing Kedro within a virtual environment, which, as I realized later, was the approach that you suggest in the tutorial. I guess the problem was due to conflicts between Python packages installed via apt and those installed via pip

lorenabalan commented 4 years ago

Glad to hear it's working now! I'll go ahead and close this issue in that case. :)