Installation issue
praksharma opened this issue · comments
So, I am using Python 3.7.2 on a HPC cluster. The package versions are conflicting. So, pip can;t install numpy and setuptools. Which python version do you guys recommend me to use? I want to run the "learning to simulate" code.
(env) [s.1915438@sl1(sunbird) deepmind-research]$ cmake --version
cmake version 3.14.3
CMake suite maintained and supported by Kitware (kitware.com/cmake).
(env) [s.1915438@sl1(sunbird) deepmind-research]$ pip install -r learning_to_simulate/requirements.txt
Looking in indexes: https://pypi.org/simple, https://pypi.ngc.nvidia.com
Requirement already satisfied: absl-py in ./env/lib/python3.7/site-packages (from -r learning_to_simulate/requirements.txt (line 1)) (1.4.0)
Collecting graph-nets>=1.1 (from -r learning_to_simulate/requirements.txt (line 2))
Downloading https://files.pythonhosted.org/packages/47/7a/a4a686426b1eae92887280d008c92bac2a0d1ed7dfa083a277d64f47555f/graph_nets-1.1.0.tar.gz (76kB)
100% |████████████████████████████████| 81kB 11.2MB/s
Collecting tensorflow<2,>=1.15 (from -r learning_to_simulate/requirements.txt (line 3))
Downloading https://files.pythonhosted.org/packages/9a/51/99abd43185d94adaaaddf8f44a80c418a91977924a7bc39b8dacd0c495b0/tensorflow-1.15.5-cp37-cp37m-manylinux2010_x86_64.whl (110.5MB)
100% |████████████████████████████████| 110.5MB 64.9MB/s
Requirement already satisfied: numpy in /lustrehome/apps/local/languages/python/3.7.2/gnu-8.1/lib/python3.7/site-packages (from -r learning_to_simulate/requirements.txt (line 4)) (1.20.1)
Requirement already satisfied: dm-sonnet<2 in ./env/lib/python3.7/site-packages (from -r learning_to_simulate/requirements.txt (line 5)) (1.36)
Requirement already satisfied: tensorflow_probability<0.9 in ./env/lib/python3.7/site-packages (from -r learning_to_simulate/requirements.txt (line 6)) (0.8.0)
Collecting sklearn (from -r learning_to_simulate/requirements.txt (line 7))
Downloading https://files.pythonhosted.org/packages/7a/93/e0e1b1e98f39dfca7ec9795cb46f6e09e88a2fd5d4a28e4b3d1f618a2aec/sklearn-0.0.post5.tar.gz
Collecting dm-tree (from -r learning_to_simulate/requirements.txt (line 8))
Downloading https://files.pythonhosted.org/packages/f8/6d/f1997aac42e0f550c1e952a0b920eaa0bfc4d27d0421499881b934b969fc/dm-tree-0.1.8.tar.gz
Requirement already satisfied: matplotlib in /lustrehome/apps/local/languages/python/3.7.2/gnu-8.1/lib/python3.7/site-packages (from -r learning_to_simulate/requirements.txt (line 9)) (3.0.2)
Collecting future (from graph-nets>=1.1->-r learning_to_simulate/requirements.txt (line 2))
Downloading https://files.pythonhosted.org/packages/8f/2e/cf6accf7415237d6faeeebdc7832023c90e0282aa16fd3263db0eb4715ec/future-0.18.3.tar.gz (840kB)
100% |████████████████████████████████| 849kB 77.0MB/s
Requirement already satisfied: networkx in /lustrehome/apps/local/languages/python/3.7.2/gnu-8.1/lib/python3.7/site-packages (from graph-nets>=1.1->-r learning_to_simulate/requirements.txt (line 2)) (2.5)
Requirement already satisfied: setuptools in /lustrehome/apps/local/languages/python/3.7.2/gnu-8.1/lib/python3.7/site-packages (from graph-nets>=1.1->-r learning_to_simulate/requirements.txt (line 2)) (40.6.2)
Requirement already satisfied: six in /lustrehome/apps/local/languages/python/3.7.2/gnu-8.1/lib/python3.7/site-packages (from graph-nets>=1.1->-r learning_to_simulate/requirements.txt (line 2)) (1.12.0)
Collecting grpcio>=1.8.6 (from tensorflow<2,>=1.15->-r learning_to_simulate/requirements.txt (line 3))
Downloading https://files.pythonhosted.org/packages/76/63/d025fb7599379765d6437e5aab3644955248ea89d2f84f4f8a9762d99c52/grpcio-1.55.0.tar.gz (24.2MB)
100% |████████████████████████████████| 24.2MB 76.9MB/s
Collecting opt-einsum>=2.3.2 (from tensorflow<2,>=1.15->-r learning_to_simulate/requirements.txt (line 3))
Downloading https://files.pythonhosted.org/packages/bc/19/404708a7e54ad2798907210462fd950c3442ea51acc8790f3da48d2bee8b/opt_einsum-3.3.0-py3-none-any.whl (65kB)
100% |████████████████████████████████| 71kB 54.1MB/s
Collecting google-pasta>=0.1.6 (from tensorflow<2,>=1.15->-r learning_to_simulate/requirements.txt (line 3))
Downloading https://files.pythonhosted.org/packages/a3/de/c648ef6835192e6e2cc03f40b19eeda4382c49b5bafb43d88b931c4c74ac/google_pasta-0.2.0-py3-none-any.whl (57kB)
100% |████████████████████████████████| 61kB 52.4MB/s
Collecting protobuf>=3.6.1 (from tensorflow<2,>=1.15->-r learning_to_simulate/requirements.txt (line 3))
Downloading https://files.pythonhosted.org/packages/1d/af/4e351c0157d5a0440dc3ac0b3c1fdaa036b3b446bf98310b5e3d6d9d2733/protobuf-4.23.2-py3-none-any.whl (173kB)
100% |████████████████████████████████| 174kB 87.7MB/s
Collecting wheel>=0.26; python_version >= "3" (from tensorflow<2,>=1.15->-r learning_to_simulate/requirements.txt (line 3))
Downloading https://files.pythonhosted.org/packages/61/86/cc8d1ff2ca31a312a25a708c891cf9facbad4eae493b3872638db6785eb5/wheel-0.40.0-py3-none-any.whl (64kB)
100% |████████████████████████████████| 71kB 70.6MB/s
Requirement already satisfied: gast==0.2.2 in ./env/lib/python3.7/site-packages (from tensorflow<2,>=1.15->-r learning_to_simulate/requirements.txt (line 3)) (0.2.2)
Requirement already satisfied: h5py<=2.10.0 in /lustrehome/apps/local/languages/python/3.7.2/gnu-8.1/lib/python3.7/site-packages (from tensorflow<2,>=1.15->-r learning_to_simulate/requirements.txt (line 3)) (2.9.0)
Collecting keras-preprocessing>=1.0.5 (from tensorflow<2,>=1.15->-r learning_to_simulate/requirements.txt (line 3))
Downloading https://files.pythonhosted.org/packages/79/4c/7c3275a01e12ef9368a892926ab932b33bb13d55794881e3573482b378a7/Keras_Preprocessing-1.1.2-py2.py3-none-any.whl (42kB)
100% |████████████████████████████████| 51kB 58.4MB/s
Collecting keras-applications>=1.0.8 (from tensorflow<2,>=1.15->-r learning_to_simulate/requirements.txt (line 3))
Downloading https://files.pythonhosted.org/packages/71/e3/19762fdfc62877ae9102edf6342d71b28fbfd9dea3d2f96a882ce099b03f/Keras_Applications-1.0.8-py3-none-any.whl (50kB)
100% |████████████████████████████████| 51kB 56.0MB/s
Collecting termcolor>=1.1.0 (from tensorflow<2,>=1.15->-r learning_to_simulate/requirements.txt (line 3))
Downloading https://files.pythonhosted.org/packages/67/e1/434566ffce04448192369c1a282931cf4ae593e91907558eaecd2e9f2801/termcolor-2.3.0-py3-none-any.whl
Collecting astor>=0.6.0 (from tensorflow<2,>=1.15->-r learning_to_simulate/requirements.txt (line 3))
Downloading https://files.pythonhosted.org/packages/c3/88/97eef84f48fa04fbd6750e62dcceafba6c63c81b7ac1420856c8dcc0a3f9/astor-0.8.1-py2.py3-none-any.whl
Requirement already satisfied: wrapt>=1.11.1 in ./env/lib/python3.7/site-packages (from tensorflow<2,>=1.15->-r learning_to_simulate/requirements.txt (line 3)) (1.15.0)
Collecting tensorboard<1.16.0,>=1.15.0 (from tensorflow<2,>=1.15->-r learning_to_simulate/requirements.txt (line 3))
Downloading https://files.pythonhosted.org/packages/1e/e9/d3d747a97f7188f48aa5eda486907f3b345cd409f0a0850468ba867db246/tensorboard-1.15.0-py3-none-any.whl (3.8MB)
100% |████████████████████████████████| 3.8MB 75.0MB/s
Collecting tensorflow-estimator==1.15.1 (from tensorflow<2,>=1.15->-r learning_to_simulate/requirements.txt (line 3))
Downloading https://files.pythonhosted.org/packages/de/62/2ee9cd74c9fa2fa450877847ba560b260f5d0fb70ee0595203082dafcc9d/tensorflow_estimator-1.15.1-py2.py3-none-any.whl (503kB)
100% |████████████████████████████████| 512kB 81.6MB/s
Requirement already satisfied: contextlib2 in ./env/lib/python3.7/site-packages (from dm-sonnet<2->-r learning_to_simulate/requirements.txt (line 5)) (21.6.0)
Requirement already satisfied: semantic-version in ./env/lib/python3.7/site-packages (from dm-sonnet<2->-r learning_to_simulate/requirements.txt (line 5)) (2.10.0)
Requirement already satisfied: cloudpickle==1.1.1 in ./env/lib/python3.7/site-packages (from tensorflow_probability<0.9->-r learning_to_simulate/requirements.txt (line 6)) (1.1.1)
Requirement already satisfied: decorator in /lustrehome/apps/local/languages/python/3.7.2/gnu-8.1/lib/python3.7/site-packages (from tensorflow_probability<0.9->-r learning_to_simulate/requirements.txt (line 6)) (4.3.2)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /lustrehome/apps/local/languages/python/3.7.2/gnu-8.1/lib/python3.7/site-packages (from matplotlib->-r learning_to_simulate/requirements.txt (line 9)) (2.3.1)
Requirement already satisfied: cycler>=0.10 in /lustrehome/apps/local/languages/python/3.7.2/gnu-8.1/lib/python3.7/site-packages (from matplotlib->-r learning_to_simulate/requirements.txt (line 9)) (0.10.0)
Requirement already satisfied: python-dateutil>=2.1 in /lustrehome/apps/local/languages/python/3.7.2/gnu-8.1/lib/python3.7/site-packages (from matplotlib->-r learning_to_simulate/requirements.txt (line 9)) (2.8.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /lustrehome/apps/local/languages/python/3.7.2/gnu-8.1/lib/python3.7/site-packages (from matplotlib->-r learning_to_simulate/requirements.txt (line 9)) (1.0.1)
Collecting markdown>=2.6.8 (from tensorboard<1.16.0,>=1.15.0->tensorflow<2,>=1.15->-r learning_to_simulate/requirements.txt (line 3))
Downloading https://files.pythonhosted.org/packages/9a/a1/1352b0e5a3c71a79fa9265726e2217f69df9fd4de0bcb5725cc61f62a5df/Markdown-3.4.3-py3-none-any.whl (93kB)
100% |████████████████████████████████| 102kB 64.8MB/s
Collecting werkzeug>=0.11.15 (from tensorboard<1.16.0,>=1.15.0->tensorflow<2,>=1.15->-r learning_to_simulate/requirements.txt (line 3))
Downloading https://files.pythonhosted.org/packages/f6/f8/9da63c1617ae2a1dec2fbf6412f3a0cfe9d4ce029eccbda6e1e4258ca45f/Werkzeug-2.2.3-py3-none-any.whl (233kB)
100% |████████████████████████████████| 235kB 83.2MB/s
Collecting importlib-metadata>=4.4; python_version < "3.10" (from markdown>=2.6.8->tensorboard<1.16.0,>=1.15.0->tensorflow<2,>=1.15->-r learning_to_simulate/requirements.txt (line 3))
Downloading https://files.pythonhosted.org/packages/30/bb/bf2944b8b88c65b797acc2c6a2cb0fb817f7364debf0675792e034013858/importlib_metadata-6.6.0-py3-none-any.whl
Collecting MarkupSafe>=2.1.1 (from werkzeug>=0.11.15->tensorboard<1.16.0,>=1.15.0->tensorflow<2,>=1.15->-r learning_to_simulate/requirements.txt (line 3))
Downloading https://files.pythonhosted.org/packages/6d/7c/59a3248f411813f8ccba92a55feaac4bf360d29e2ff05ee7d8e1ef2d7dbf/MarkupSafe-2.1.3.tar.gz
Collecting typing-extensions>=3.6.4; python_version < "3.8" (from importlib-metadata>=4.4; python_version < "3.10"->markdown>=2.6.8->tensorboard<1.16.0,>=1.15.0->tensorflow<2,>=1.15->-r learning_to_simulate/requirements.txt (line 3))
Downloading https://files.pythonhosted.org/packages/5f/86/d9b1518d8e75b346a33eb59fa31bdbbee11459a7e2cc5be502fa779e96c5/typing_extensions-4.6.3-py3-none-any.whl
Collecting zipp>=0.5 (from importlib-metadata>=4.4; python_version < "3.10"->markdown>=2.6.8->tensorboard<1.16.0,>=1.15.0->tensorflow<2,>=1.15->-r learning_to_simulate/requirements.txt (line 3))
Downloading https://files.pythonhosted.org/packages/5b/fa/c9e82bbe1af6266adf08afb563905eb87cab83fde00a0a08963510621047/zipp-3.15.0-py3-none-any.whl
tensorboard 1.15.0 has requirement setuptools>=41.0.0, but you'll have setuptools 40.6.2 which is incompatible.
tensorflow 1.15.5 has requirement numpy<1.19.0,>=1.16.0, but you'll have numpy 1.20.1 which is incompatible.
Installing collected packages: dm-tree, future, graph-nets, grpcio, opt-einsum, google-pasta, protobuf, wheel, keras-preprocessing, keras-applications, termcolor, astor, typing-extensions, zipp, importlib-metadata, markdown, MarkupSafe, werkzeug, tensorboard, tensorflow-estimator, tensorflow, sklearn
Running setup.py install for dm-tree ... done
Running setup.py install for future ... done
Running setup.py install for graph-nets ... done
Running setup.py install for grpcio ... done
Running setup.py install for MarkupSafe ... done
Running setup.py install for sklearn ... error
Complete output from command /scratch/s.1915438/deepmind/deepmind-research/env/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-chjnre06/sklearn/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-5ttw92cq/install-record.txt --single-version-externally-managed --compile --install-headers /scratch/s.1915438/deepmind/deepmind-research/env/include/site/python3.7/sklearn:
The 'sklearn' PyPI package is deprecated, use 'scikit-learn'
rather than 'sklearn' for pip commands.
Here is how to fix this error in the main use cases:
- use 'pip install scikit-learn' rather than 'pip install sklearn'
- replace 'sklearn' by 'scikit-learn' in your pip requirements files
(requirements.txt, setup.py, setup.cfg, Pipfile, etc ...)
- if the 'sklearn' package is used by one of your dependencies,
it would be great if you take some time to track which package uses
'sklearn' instead of 'scikit-learn' and report it to their issue tracker
- as a last resort, set the environment variable
SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True to avoid this error
More information is available at
https://github.com/scikit-learn/sklearn-pypi-package
If the previous advice does not cover your use case, feel free to report it at
https://github.com/scikit-learn/sklearn-pypi-package/issues/new
----------------------------------------
Command "/scratch/s.1915438/deepmind/deepmind-research/env/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-chjnre06/sklearn/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-5ttw92cq/install-record.txt --single-version-externally-managed --compile --install-headers /scratch/s.1915438/deepmind/deepmind-research/env/include/site/python3.7/sklearn" failed with error code 1 in /tmp/pip-install-chjnre06/sklearn/
You are using pip version 19.0.2, however version 23.1.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
(env) [s.1915438@sl1(sunbird) deepmind-research]$