メインサーバ（RX1330M3）
$ which python3 /home/linuxbrew/.linuxbrew/bin/python3 $ python3 --version Python 3.9.7 $ python3 -m pip list Package Version --------------------- --------- alembic 1.7.1 beautifulsoup4 4.10.0 biopython 1.79 bleach 4.1.0 bokeh 2.3.3 certifi 2021.5.30 charset-normalizer 2.0.4 click 8.0.1 configparser 5.0.2 cycler 0.10.0 dominate 2.6.0 Flask 1.1.2 Flask-Bootstrap 3.3.7.1 flask-ldap3-login 0.9.16 Flask-Login 0.5.0 Flask-Migrate 3.1.0 Flask-Moment 1.0.2 Flask-Script 2.0.6 Flask-SQLAlchemy 2.5.1 Flask-WTF 0.15.1 greenlet 1.1.1 idna 3.2 itsdangerous 2.0.1 Jinja2 3.0.1 joblib 1.0.1 kiwisolver 1.3.2 ldap3 2.9.1 libxml2-python 2.9.12 Mako 1.1.5 Markdown 3.3.4 MarkupSafe 2.0.1 matplotlib 3.4.3 meson 0.59.1 msgpack-python 0.5.6 msgpack-tool 0.0.1 numpy 1.21.2 packaging 21.0 pandas 1.3.2 panel 0.12.1 param 1.11.1 patsy 0.5.1 Pillow 8.3.2 pip 21.2.4 pyasn1 0.4.8 pyct 0.4.8 PyMySQL 1.0.2 pyparsing 2.4.7 PyQt3D 5.15.4 PyQt5 5.15.4 PyQt5-sip 12.9.0 PyQtChart 5.15.4 PyQtDataVisualization 5.15.4 PyQtNetworkAuth 5.15.4 PyQtPurchasing 5.15.4 pysam 0.16.0.1 python-dateutil 2.8.2 pytz 2021.1 PyVCF 0.6.8 pyviz-comms 2.1.0 PyYAML 5.4.1 regex 2021.8.28 requests 2.26.0 scikit-learn 0.24.2 scipy 1.7.1 seaborn 0.11.2 setuptools 57.4.0 sip 6.1.1 six 1.16.0 sklearn 0.0 soupsieve 2.2.1 SQLAlchemy 1.4.23 statsmodels 0.12.2 TBB 0.2 threadpoolctl 2.2.0 toml 0.10.2 tornado 6.1 tqdm 4.62.2 typing-extensions 3.10.0.2 urllib3 1.26.6 visitor 0.1.3 webencodings 0.5.1 Werkzeug 2.0.1 wheel 0.37.0 WTForms 2.3.3
GPUサーバ（TX1310M3)
$ which python3 /home/linuxbrew/.linuxbrew/bin/python3 $ python3 --version Python 3.9.6 $ python3 -m pip list Package Version --------------------------------- ------- backports.entry-points-selectable 1.1.0 distlib 0.3.2 filelock 3.0.12 pip 21.2.4 platformdirs 2.2.0 setuptools 57.0.0 six 1.16.0 virtualenv 20.7.2 wheel 0.36.2
virtualenvで環境切り分け
Alphafold2(Docker)用として使うときは
$ cd ~/alphafold $ source alphafold/bin/activate $ python3 -m pip list Package Version ----------------------- ------------------- absl-py 0.13.0 astunparse 1.6.3 biopython 1.79 cachetools 4.2.2 certifi 2021.5.30 charset-normalizer 2.0.4 chex 0.0.7 contextlib2 21.6.0 dm-haiku 0.0.4 dm-tree 0.1.6 docker 5.0.0 flatbuffers 1.12 gast 0.4.0 google-auth 1.35.0 google-auth-oauthlib 0.4.5 google-pasta 0.2.0 grpcio 1.34.1 h5py 3.1.0 idna 3.2 immutabledict 2.0.0 jax 0.2.14 jaxlib 0.1.70 keras-nightly 2.5.0.dev2021032900 Keras-Preprocessing 1.1.2 Markdown 3.3.4 ml-collections 0.1.0 numpy 1.19.5 oauthlib 3.1.1 opt-einsum 3.3.0 pip 21.2.4 protobuf 3.17.3 pyasn1 0.4.8 pyasn1-modules 0.2.8 PyYAML 5.4.1 requests 2.26.0 requests-oauthlib 1.3.0 rsa 4.7.2 scipy 1.7.0 setuptools 57.4.0 six 1.15.0 tabulate 0.8.9 tensorboard 2.6.0 tensorboard-data-server 0.6.1 tensorboard-plugin-wit 1.8.0 tensorflow-cpu 2.5.0 tensorflow-estimator 2.5.0 termcolor 1.1.0 toolz 0.11.1 typing-extensions 3.7.4.3 urllib3 1.26.6 websocket-client 1.2.1 Werkzeug 2.0.1 wheel 0.37.0 wrapt 1.12.1
のように切り替える。
Mac mini (2018)
$ which python3 /usr/local/bin/python3 #brewで入れたpython3 $ python3 --version Python 3.9.6 $ python3 -m pip list Package Version ----------------------- ------- mmtf-python 1.1.2 msgpack 1.0.2 numpy 1.21.2 packaging 20.9 pip 21.1.3 Pmw 2.1 pymol 2.4.0 pyparsing 2.4.7 PyQt3D 5.15.4 PyQt5 5.15.4 PyQt5-sip 12.9.0 PyQt6 6.1.1 PyQt6-3D 6.1.1 PyQt6-Charts 6.1.1 PyQt6-DataVisualization 6.1.1 PyQt6-NetworkAuth 6.1.1 PyQt6-sip 13.1.0 PyQtChart 5.15.4 PyQtDataVisualization 5.15.4 PyQtNetworkAuth 5.15.4 PyQtPurchasing 5.15.4 PyQtWebEngine 5.15.4 setuptools 57.0.0 sip 6.1.1 TBB 0.2 toml 0.10.2 wheel 0.36.2
MacBook Air (Retina, 13-inch, 2020)
% which python3 /Users/kuro/.pyenv/shims/python3 % pyenv versions system * 3.8.6 (set by /Users/kuro/.pyenv/version) anaconda3-5.3.1 anaconda3-5.3.1/envs/usml % python3 --version Python 3.8.6 % python3 -m pip list Package Version ------------------- ------- appnope 0.1.1 argon2-cffi 20.1.0 async-generator 1.10 attrs 20.3.0 backcall 0.2.0 biopython 1.78 bleach 3.2.1 cffi 1.14.4 click 7.1.2 cycler 0.10.0 decorator 4.4.2 defusedxml 0.6.0 entrypoints 0.3 Flask 1.1.2 greenlet 1.0.0 ipykernel 5.3.4 ipython 7.19.0 ipython-genutils 0.2.0 ipywidgets 7.5.1 itsdangerous 1.1.0 jedi 0.17.2 Jinja2 2.11.2 joblib 0.17.0 jsonschema 3.2.0 jupyter 1.0.0 jupyter-client 6.1.7 jupyter-console 6.2.0 jupyter-core 4.7.0 jupyterlab-pygments 0.1.2 kiwisolver 1.3.1 MarkupSafe 1.1.1 matplotlib 3.3.3 mistune 0.8.4 nbclient 0.5.1 nbconvert 6.0.7 nbformat 5.0.8 nest-asyncio 1.4.3 notebook 6.1.5 numpy 1.19.4 packaging 20.7 pandas 1.1.4 pandocfilters 1.4.3 parso 0.7.1 patsy 0.5.1 pexpect 4.8.0 pickleshare 0.7.5 Pillow 8.0.1 pip 21.2.4 prometheus-client 0.9.0 prompt-toolkit 3.0.8 ptyprocess 0.6.0 pycparser 2.20 Pygments 2.7.2 pyparsing 2.4.7 pyrsistent 0.17.3 python-dateutil 2.8.1 pytz 2020.4 pyzmq 20.0.0 qtconsole 5.0.1 QtPy 1.9.0 scikit-learn 0.23.2 scipy 1.5.4 seaborn 0.11.0 Send2Trash 1.5.0 setuptools 49.2.1 six 1.15.0 sklearn 0.0 somoclu 1.7.5 SQLAlchemy 1.4.4 statsmodels 0.12.1 terminado 0.9.1 testpath 0.4.4 threadpoolctl 2.1.0 tornado 6.1 traitlets 5.0.5 wcwidth 0.2.5 webencodings 0.5.1 Werkzeug 1.0.1 widgetsnbextension 3.5.1
pyenvをbrewでインストールしている。
通常は3.8.6で、機械学習のテスト用にanaconda3-5.3.1(Python 3.7.0)をインストール。
% pyenv global anaconda3-5.3.1/envs/usml % pyenv versions system 3.8.6 anaconda3-5.3.1 * anaconda3-5.3.1/envs/usml (set by /Users/kuro/.pyenv/version) % python --version Python 3.6.10 :: Anaconda, Inc. % python3 -m pip list Package Version ---------------------------------- ------------------- alabaster 0.7.12 anaconda-client 1.7.2 anaconda-project 0.8.3 applaunchservices 0.2.1 appnope 0.1.0 appscript 1.1.1 argh 0.26.2 asn1crypto 1.3.0 astroid 2.4.2 astropy 4.0.1.post1 atomicwrites 1.4.0 attrs 19.3.0 autopep8 1.5.3 Babel 2.8.0 backcall 0.2.0 backports.shutil-get-terminal-size 1.0.0 beautifulsoup4 4.9.1 bitarray 1.4.0 bkcharts 0.2 bleach 3.1.5 bokeh 2.1.1 boto 2.49.0 Bottleneck 1.3.2 brotlipy 0.7.0 certifi 2020.6.20 cffi 1.14.0 chardet 3.0.4 click 7.1.2 cloudpickle 1.5.0 clyent 1.2.2 colorama 0.4.3 contextlib2 0.6.0.post1 contextvars 2.4 cryptography 2.9.2 cycler 0.10.0 Cython 0.29.21 cytoolz 0.10.1 dask 2.20.0 decorator 4.4.2 defusedxml 0.6.0 diff-match-patch 20200713 distributed 2.20.0 docutils 0.16 entrypoints 0.3 et-xmlfile 1.0.1 fastcache 1.1.0 filelock 3.0.12 flake8 3.8.3 Flask 1.1.2 fsspec 0.7.4 future 0.18.2 gevent 20.6.2 glob2 0.7 gmpy2 2.0.8 greenlet 0.4.16 h5py 2.10.0 HeapDict 1.0.1 html5lib 1.1 idna 2.10 imageio 2.9.0 imagesize 1.2.0 immutables 0.14 importlib-metadata 1.7.0 intervaltree 3.0.2 ipykernel 5.3.2 ipython 7.16.1 ipython-genutils 0.2.0 ipywidgets 7.5.1 isort 4.3.21 itsdangerous 1.1.0 jdcal 1.4.1 jedi 0.17.1 Jinja2 2.11.2 joblib 0.16.0 json5 0.9.5 jsonschema 3.2.0 jupyter 1.0.0 jupyter-client 6.1.6 jupyter-console 6.1.0 jupyter-core 4.6.3 jupyterlab 2.1.5 jupyterlab-server 1.2.0 keyring 21.2.1 kiwisolver 1.2.0 lazy-object-proxy 1.4.3 libarchive-c 2.9 llvmlite 0.33.0+1.g022ab0f locket 0.2.0 lxml 4.5.2 MarkupSafe 1.1.1 matplotlib 3.2.2 mccabe 0.6.1 mistune 0.8.4 mkl-fft 1.0.14 mkl-random 1.0.4 mkl-service 2.3.0 mock 4.0.2 more-itertools 8.4.0 mpmath 1.1.0 msgpack 1.0.0 multipledispatch 0.6.0 nbconvert 5.6.1 nbformat 5.0.7 networkx 2.4 nltk 3.5 nose 1.3.7 notebook 6.0.3 numba 0.50.1 numexpr 2.7.1 numpy 1.17.0 numpydoc 1.1.0 olefile 0.46 openpyxl 3.0.4 packaging 20.4 pandas 1.0.5 pandocfilters 1.4.2 parso 0.7.0 partd 1.1.0 path 13.1.0 pathlib2 2.3.5 pathtools 0.1.2 patsy 0.5.1 pep8 1.7.1 pexpect 4.8.0 pickleshare 0.7.5 Pillow 7.2.0 pip 20.1.1 pkginfo 1.5.0.1 pluggy 0.13.1 ply 3.11 prometheus-client 0.8.0 prompt-toolkit 3.0.5 psutil 5.7.0 ptyprocess 0.6.0 py 1.9.0 pycodestyle 2.6.0 pycosat 0.6.3 pycparser 2.20 pycrypto 2.6.1 pycurl 7.43.0.5 pydocstyle 5.0.2 pyflakes 2.2.0 Pygments 2.6.1 pylint 2.5.3 pyodbc 4.0.0-unsupported pyOpenSSL 19.1.0 pyparsing 2.4.7 pyrsistent 0.16.0 PySocks 1.7.1 pytest 5.4.3 python-dateutil 2.8.1 python-jsonrpc-server 0.3.4 python-language-server 0.34.1 pytz 2020.1 PyWavelets 1.1.1 PyYAML 5.3.1 pyzmq 19.0.1 QDarkStyle 2.8.1 QtAwesome 0.7.2 qtconsole 4.7.5 QtPy 1.9.0 regex 2020.6.8 requests 2.24.0 rope 0.17.0 Rtree 0.9.4 ruamel-yaml 0.15.87 scikit-image 0.16.2 scikit-learn 0.23.1 scipy 1.5.0 seaborn 0.10.1 Send2Trash 1.5.0 setuptools 49.2.0.post20200714 simplegeneric 0.8.1 singledispatch 3.4.0.3 six 1.15.0 snowballstemmer 2.0.0 sortedcollections 1.2.1 sortedcontainers 2.2.2 soupsieve 2.0.1 Sphinx 3.1.2 sphinxcontrib-applehelp 1.0.2 sphinxcontrib-devhelp 1.0.2 sphinxcontrib-htmlhelp 1.0.3 sphinxcontrib-jsmath 1.0.1 sphinxcontrib-qthelp 1.0.3 sphinxcontrib-serializinghtml 1.1.4 sphinxcontrib-websupport 1.2.3 spyder 4.1.4 spyder-kernels 1.9.2 SQLAlchemy 1.3.18 statsmodels 0.11.1 sympy 1.6.1 tables 3.6.1 tblib 1.6.0 terminado 0.8.3 testpath 0.4.4 threadpoolctl 2.1.0 toml 0.10.1 toolz 0.10.0 tornado 6.0.4 tqdm 4.47.0 traitlets 4.3.3 typed-ast 1.4.1 typing-extensions 3.7.4.2 ujson 1.35 unicodecsv 0.14.1 urllib3 1.25.9 watchdog 0.10.3 wcwidth 0.2.5 webencodings 0.5.1 Werkzeug 1.0.1 wheel 0.34.2 widgetsnbextension 3.5.1 wrapt 1.11.2 wurlitzer 2.0.1 xlrd 1.2.0 XlsxWriter 1.2.9 xlwings 0.19.5 xlwt 1.2.0 yapf 0.30.0 zict 2.0.0 zipp 3.1.0 zope.event 4.4 zope.interface 4.7.1
