diff --git a/HPC_setup/mlt_modules_juwels.sh b/HPC_setup/mlt_modules_juwels.sh index ffacfe6fc45302dfa60b108ca2493d9a27408df1..e72c0f63141bad4bab442e18b93d9fbb37adb287 100755 --- a/HPC_setup/mlt_modules_juwels.sh +++ b/HPC_setup/mlt_modules_juwels.sh @@ -11,7 +11,7 @@ module use $OTHERSTAGES ml Stages/2020 ml GCCcore/.10.3.0 -ml Jupyter/2021.3.1-Python-3.8.5 +# ml Jupyter/2021.3.1-Python-3.8.5 ml Python/3.8.5 ml TensorFlow/2.5.0-Python-3.8.5 ml SciPy-Stack/2021-Python-3.8.5 diff --git a/requirements.txt b/requirements.txt index 701b7cb99577bda777058211e966ae1618b8754c..6da10111d77504efb5d17359df4502e748f1aa39 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,263 +1,96 @@ -## this is basically the "pip list --format=freeze" output from a fully loaded venv_juwels ## - absl-py==0.12.0 -aiohttp==3.6.2 -alabaster==0.7.12 +aiohttp==3.7.4 alembic==1.4.2 -altair==3.3.0 -ansi2html==1.5.2 -ansiwrap==0.8.4 -anyio==3.2.1 apipkg==1.5 appdirs==1.4.4 -appmode==0.6.0 argcomplete==1.12.0 -argon2-cffi==20.1.0 -arviz==0.10.0 asn1crypto==1.3.0 astor==0.8.1 -astroid==2.4.2 astropy==4.1 astunparse==1.6.3 -async-generator==1.10 -async-timeout==3.0.1 atomicwrites==1.4.0 attrs==19.3.0 -autobahn==19.10.1 -Automat==0.8.0 -autopep8==1.4.4 -Babel==2.7.0 backcall==0.2.0 backports.shutil-get-terminal-size==1.0.0 -backports.tempfile==1.0 -backports.weakref==1.0.post1 bcrypt==3.1.7 bitstring==3.1.7 -black==19.3b0 -bleach==3.3.0 blist==1.3.6 -bokeh==2.3.2 Bottleneck==1.3.2 -bqplot==0.12.26 -CacheControl==0.12.6 cached-property==1.5.2 cachetools==4.2.2 -cachy==0.3.0 certifi==2020.6.20 -certipy==0.1.3 cffi==1.14.1 -cftime==1.2.1 +cftime==1.4.1 chardet==3.0.4 -cleo==0.8.1 click==7.1.2 -clikit==0.6.2 -cloudpickle==1.6.0 +cloudpickle==1.5.0 ClusterShell==1.8.3 -colorama==0.4.1 -colorcet==2.0.2 -commonmark==0.9.1 configparser==5.0.0 -constantly==15.1.0 coverage==5.1 -crashtest==0.3.1 cryptography==3.0 -cssselect==1.1.0 cycler==0.10.0 Cython==0.29.21 -dash==1.16.0 -dash-bio==0.4.8 -dash-bootstrap-components==0.10.5 -dash-canvas==0.1.0 -dash-core-components==1.12.0 -dash-cytoscape==0.2.0 -dash-daq==0.5.0 -dash-html-components==1.1.1 -dash-player==0.0.1 -dash-renderer==1.8.0 -dash-table==4.10.1 -dask -datashader==0.11.1 -datashape==0.5.2 +dask==2.22.0 deap==1.3.1 -debugpy==1.4.0 decorator==4.4.2 -defusedxml==0.6.0 -deprecation==2.1.0 -dicom-upload==0.2.0 dill==0.3.3 -distlib==0.3.1 -distributed==2.30.1 -distro==1.5.0 -docutils==0.15.2 ecdsa==0.15 -entrypoints==0.3 execnet==1.7.1 -fastcore==1.3.6 -fastscript==1.0.0 -filelock==3.0.12 -flake8==3.8.3 Flask==1.1.2 -Flask-Caching==1.9.0 -Flask-Compress==1.4.0 flatbuffers==1.12 -flit-core==3.2.0 -fsspec==0.6.2 +fsspec==0.8.5 funcsigs==1.0.2 future==0.18.2 gast==0.4.0 -gitdb2==2.0.6 -GitPython==3.0.4 google-auth==1.30.0 google-auth-oauthlib==0.4.4 google-pasta==0.2.0 grako==3.99.9 -graphviz==0.13.2 grpcio==1.34.1 gviz-api==1.9.0 h5py==3.1.0 -HeapDict==1.0.1 -hiredis==1.1.0 -holoviews==1.13.2 html5lib==1.1 -hyperlink==19.0.0 hypothesis==4.44.2 -icc-rt==2020.0.133 idna==2.10 -idna-ssl==1.1.0 -imageio==2.9.0 -imagesize==1.1.0 -importlib-metadata==3.4.0 -incremental==17.5.0 iniconfig==1.1.1 -intel-openmp==2020.0.133 ipaddress==1.0.23 -ipydatawidgets==4.2.0 -ipykernel==6.0.3 -ipyleaflet==0.14.0 -ipympl==0.7.0 -ipynb==0.5.1 -ipyparallel==6.3.0 ipython==7.16.1 ipython-genutils==0.2.0 -ipythonblocks==1.9.0 -ipyvolume==0.6.0a8 -ipyvue==1.5.0 -ipyvuetify==1.6.2 -ipywebrtc==0.6.0 -ipywidgets==7.6.3 isodate==0.6.0 -isort==4.3.21 -itk-core==5.2.1 -itk-filtering==5.2.1 -itk-io==5.2.1 -itk-meshtopolydata==0.7.1 -itk-numerics==5.2.1 -itk-registration==5.2.1 -itk-segmentation==5.2.1 itsdangerous==1.1.0 jedi==0.17.2 -jeepney==0.6.0 Jinja2==2.11.2 -joblib==0.17.0 -jsfileupload==0.2.0 -json5==0.8.5 jsonschema==3.2.0 -jupyter-bokeh==3.0.0 -jupyter-client==6.1.12 -jupyter-contrib-core==0.3.3 -jupyter-contrib-nbextensions==0.5.1 -jupyter-core==4.8.1 -jupyter-dash==0.4.0 -jupyter-highlight-selected-word==0.2.0 -jupyter-kernel-gateway==2.5.1 -jupyter-latex-envs==1.4.6 -jupyter-lsp==1.4.1 -jupyter-nbextensions-configurator==0.4.1 -jupyter-packaging==0.10.5 -jupyter-resource-usage==0.6.0 -jupyter-server==1.11.0 -jupyter-server-mathjax==0.2.3 -jupyter-server-proxy==3.1.0 -jupyter-telemetry==0.1.0 -jupyterhub==1.4.2 -jupyterlab==3.1.12 -jupyterlab-code-formatter==1.4.10 -jupyterlab-controlbtn==0.5.0 -jupyterlab-favorites==3.0.0 -jupyterlab-git==0.32.4 -jupyterlab-gitlab==3.0.0 -jupyterlab-iframe==0.4.0 -jupyterlab-latex==3.1.0 -jupyterlab-launcher==0.13.1 -jupyterlab-lsp==3.8.1 -jupyterlab-pygments==0.1.2 -jupyterlab-recents==3.0.1 -jupyterlab-server==2.8.1 -jupyterlab-spellchecker==0.7.1 -jupyterlab-system-monitor==0.8.0 -jupyterlab-topbar==0.6.1 -jupyterlab-tour==3.1.3 -jupyterlab-widgets==1.0.2 -jupyterthemes==0.20.0 keras-nightly==2.5.0.dev2021032900 Keras-Preprocessing==1.1.2 -keyring==21.8.0 kiwisolver==1.2.0 -lazy-object-proxy==1.4.3 -lesscpy==0.14.0 liac-arff==2.4.0 -line-profiler==3.1.0 -llvmlite==0.36.0 -locket==0.2.0 +locket==0.2.1 lockfile==0.12.2 lxml==4.5.2 Mako==1.1.3 Markdown==3.3.4 MarkupSafe==1.1.1 matplotlib==3.3.1 -matplotlib-inline==0.1.2 -mccabe==0.6.1 -memory-profiler==0.55.0 -mistune==0.8.4 mock==4.0.2 more-itertools==8.4.0 mpmath==1.1.0 -msgpack==1.0.0 -multidict==4.7.5 -multipledispatch==0.6.0 -nbclassic==0.3.2 -nbclient==0.5.2 -nbconvert==6.1.0 -nbdime==3.1.0 -nbformat==5.1.2 -nest-asyncio==1.5.1 +msgpack==0.6.2 netaddr==0.8.0 -netCDF4==1.5.4 +netCDF4==1.5.5.1 netifaces==0.10.9 networkx==2.4 nose==1.3.7 -notebook==6.4.3 -numba==0.53.1 -numexpr==2.7.1 numpy==1.19.4 oauthlib==3.1.0 olefile==0.46 opt-einsum==3.3.0 ordered-set==4.0.2 packaging==20.4 -pamela==1.0.0 pandas==1.1.0 -pandocfilters==1.4.3 -panel==0.9.5 -papermill==2.2.2 -param==1.9.3 paramiko==2.7.1 parso==0.7.1 -partd==1.1.0 -pastel==0.2.1 pathlib2==2.3.5 -pathspec==0.6.0 -patsy==0.5.1 paycheck==1.0.2 pbr==5.4.5 pep8==1.7.1 @@ -265,49 +98,29 @@ pexpect==4.8.0 pickleshare==0.7.5 Pillow==7.2.0 pip==20.1.1 -pkginfo==1.7.0 -plotly==4.14.3 pluggy==0.13.1 ply==3.11 -poetry==1.1.6 -poetry-core==1.0.3 portpicker==1.3.1 -prometheus-client==0.9.0 prompt-toolkit==3.0.5 protobuf==3.17.3 prov==1.5.3 psutil==5.7.2 psycopg2==2.8.5 -ptvsd==4.3.2 ptyprocess==0.6.0 -pvlink==0.3.1 py==1.9.0 pyasn1==0.4.8 pyasn1-modules==0.2.8 -pycodestyle==2.6.0 pycparser==2.20 pycrypto==2.6.1 -pyct==0.4.6 -pydicom==1.4.2 -pydocstyle==5.0.2 pydot==1.4.1 pydotplus==2.0.2 -pydub==0.23.1 -pyflakes==2.2.0 Pygments==2.6.1 -PyHamcrest==1.9.0 -PyJWT==1.7.1 -pylev==1.3.0 -pylint==2.5.3 -pymc3==3.8 PyNaCl==1.4.0 -pynvml==8.0.4 -pyOpenSSL==19.1.0 pyparsing==2.4.7 pyrsistent==0.16.0 pyshp==2.1.3 pytest==5.4.3 -pytest-cov==2.10.1 +pytest-cov==2.11.1 pytest-forked==1.3.0 pytest-html==3.1.1 pytest-lazy-fixture==0.6.3 @@ -315,75 +128,33 @@ pytest-metadata==1.11.0 pytest-runner==5.2 pytest-sugar==0.9.4 pytest-xdist==1.34.0 -pytest-xprocess==0.13.1 python-dateutil==2.8.1 -python-dotenv==0.10.3 python-editor==1.0.4 python-gflags==3.1.2 -python-json-logger==0.1.11 -python-jsonrpc-server==0.4.0 -python-lsp-jsonrpc==1.0.0 -python-lsp-server==1.1.0 python-oauth2==1.1.1 -pythreejs==2.3.0 pytz==2020.1 -pyunicore==0.9.9 -pyviz-comms==2.0.1 -PyWavelets==1.1.1 PyYAML==5.3.1 pyzmq==18.1.0 rdflib==5.0.0 -recommonmark==0.6.0 -redis==3.5.3 -regex==2019.11.1 requests==2.24.0 requests-oauthlib==1.3.0 -requests-toolbelt==0.9.1 -requests-unixsocket==0.2.0 -retrying==1.3.3 -rise==5.7.1 -rope==0.16.0 rsa==4.7.2 Rtree==0.9.4 -ruamel.yaml==0.16.5 -ruamel.yaml.clib==0.1.2 scandir==1.10.0 -scikit-build==0.11.1 -scikit-image==0.17.2 -scikit-learn==0.23.2 scipy==1.5.2 seaborn==0.10.1 -SecretStorage==3.2.0 -selenium==3.141.0 -Send2Trash==1.5.0 -service-identity==18.1.0 setuptools==47.1.0 setuptools-scm==4.1.2 -Shapely==1.7.1 -shellingham==1.4.0 -sidecar==0.5.1 -simpervisor==0.4 simplegeneric==0.8.1 simplejson==3.17.2 -singledispatch==3.4.0.3 six==1.15.0 -smmap2==2.0.5 -smopy==0.0.7 -sniffio==1.2.0 -snowballstemmer==2.0.0 -sortedcontainers==2.3.0 SPARQLWrapper==1.8.5 -Sphinx==1.8.5 -sphinx-rtd-theme==0.4.3 -sphinxcontrib-websupport==1.1.2 SQLAlchemy==1.3.18 -statsmodels==0.10.2 +statsmodels==0.12.2 sympy==1.6.1 tabulate==0.8.8 -tailer==0.4.1 TatSu==5.5.0 tblib==1.7.0 -tenacity==6.0.0 tensorboard==2.5.0 tensorboard-data-server==0.6.1 tensorboard-plugin-profile==2.4.0 @@ -391,52 +162,18 @@ tensorboard-plugin-wit==1.8.0 tensorflow==2.5.0 tensorflow-estimator==2.5.0 termcolor==1.1.0 -terminado==0.10.1 -testpath==0.4.4 -textwrap3==0.9.2 -Theano==1.0.4 -threadpoolctl==2.2.0 -tifffile==2020.10.1 -tikzplotlib==0.9.8 toml==0.10.1 -tomlkit==0.7.0 toolz==0.10.0 -tornado==6.1 -tornado-proxy-handlers==0.0.5 -tqdm==4.56.0 traitlets==4.3.3 traits==6.1.1 -traittypes==0.2.1 -Twisted==19.7.0 -txaio==18.8.1 -typed-ast==1.4.2 typing-extensions==3.7.4 -ujson==3.2.0 urllib3==1.25.10 vcversioner==2.16.0.0 -vega-datasets==0.8.0 -version-information==1.0.3 -vincent==0.4.4 -virtualenv==20.4.6 -voila==0.2.10 -voila-gridstack==0.2.0 -voila-material==0.4.0 -voila-vuetify==0.5.2 wcwidth==0.2.5 webencodings==0.5.1 -websocket-client==1.1.0 -websockify==0.9.0 Werkzeug==2.0.0 wget==3.2 wheel==0.35.0 -widgetsnbextension==3.5.1 wrapt==1.12.1 -wslink==0.1.13 -xarray==0.16.2 +xarray==0.16.0 XlsxWriter==1.2.9 -yapf==0.28.0 -yarl==1.6.3 -zict==2.0.0 -zipp==3.4.0 -zope.interface==4.7.2 -zstandard==0.12.0