Docker to run it

[smilenaderi]

is there a docker to use it? the script installation fails for me

[smilenaderi]

@patrickbryant1 @mainguyenanhvu

[patrickbryant1]

Hi, No, unfortunately only a conda (which can be built into docker). Do you have an error message?

[Sinsilcobio]

Hi, I want to install it on a server that does not allow for conda-mediated installation. Could you provide a requirements.txt file to be compatible with PIP installation?

[mainguyenanhvu]

@smilenaderi please provide me with more information about errors and your system. @Sinsilcobio let me extract pip for you.

[mainguyenanhvu]

@Sinsilcobio hope it help

absl-py==2.0.0
AmberLite==22.0
AmberUtils==21.0
annotated-types @ file:///home/conda/feedstock_root/build_artifacts/annotated-types_1696634205638/work
anyio @ file:///home/conda/feedstock_root/build_artifacts/anyio_1700835416766/work
argcomplete==3.0.8
argon2-cffi @ file:///home/conda/feedstock_root/build_artifacts/argon2-cffi_1692818318753/work
argon2-cffi-bindings @ file:///home/conda/feedstock_root/build_artifacts/argon2-cffi-bindings_1695386546427/work
arrow @ file:///home/conda/feedstock_root/build_artifacts/arrow_1696128962909/work
asttokens @ file:///home/conda/feedstock_root/build_artifacts/asttokens_1698341106958/work
astunparse @ file:///home/conda/feedstock_root/build_artifacts/astunparse_1610696312422/work
async-lru @ file:///home/conda/feedstock_root/build_artifacts/async-lru_1690563019058/work
attrs @ file:///home/conda/feedstock_root/build_artifacts/attrs_1683424013410/work
Babel @ file:///home/conda/feedstock_root/build_artifacts/babel_1702422572539/work
beautifulsoup4 @ file:///home/conda/feedstock_root/build_artifacts/beautifulsoup4_1680888073205/work
biopython==1.81
bleach @ file:///home/conda/feedstock_root/build_artifacts/bleach_1696630167146/work
Brotli @ file:///home/conda/feedstock_root/build_artifacts/brotli-split_1695989787169/work
bson==0.5.9
build==0.10.0
CacheControl==0.12.14
cached-property @ file:///home/conda/feedstock_root/build_artifacts/cached_property_1615209429212/work
cachetools @ file:///home/conda/feedstock_root/build_artifacts/cachetools_1698197297464/work
certifi @ file:///home/conda/feedstock_root/build_artifacts/certifi_1700303426725/work/certifi
cffi @ file:///home/conda/feedstock_root/build_artifacts/cffi_1696001684923/work
chardet @ file:///home/conda/feedstock_root/build_artifacts/chardet_1695468598188/work
charset-normalizer @ file:///home/conda/feedstock_root/build_artifacts/charset-normalizer_1698833585322/work
chex==0.1.5
cleo==2.0.1
colorama @ file:///home/conda/feedstock_root/build_artifacts/colorama_1666700638685/work
comm @ file:///home/conda/feedstock_root/build_artifacts/comm_1691044910542/work
contextlib2==21.6.0
contourpy @ file:///home/conda/feedstock_root/build_artifacts/contourpy_1699041363598/work
crashtest==0.4.1
cryptography @ file:///home/conda/feedstock_root/build_artifacts/cryptography-split_1701563205069/work
cycler @ file:///home/conda/feedstock_root/build_artifacts/cycler_1696677705766/work
Cython @ file:///home/conda/feedstock_root/build_artifacts/cython_1701025389997/work
debugpy @ file:///home/conda/feedstock_root/build_artifacts/debugpy_1695534290310/work
decorator @ file:///home/conda/feedstock_root/build_artifacts/decorator_1641555617451/work
defusedxml @ file:///home/conda/feedstock_root/build_artifacts/defusedxml_1615232257335/work
distlib==0.3.6
dm-haiku==0.0.9
dm-tree==0.1.8
dulwich==0.21.5
entrypoints @ file:///home/conda/feedstock_root/build_artifacts/entrypoints_1643888246732/work
exceptiongroup @ file:///home/conda/feedstock_root/build_artifacts/exceptiongroup_1700579780973/work
executing @ file:///home/conda/feedstock_root/build_artifacts/executing_1698579936712/work
fastjsonschema @ file:///home/conda/feedstock_root/build_artifacts/python-fastjsonschema_1700055509243/work/dist
filelock @ file:///home/conda/feedstock_root/build_artifacts/filelock_1698714947081/work
flatbuffers==23.5.26
fonttools @ file:///home/conda/feedstock_root/build_artifacts/fonttools_1701530662024/work
fqdn @ file:///home/conda/feedstock_root/build_artifacts/fqdn_1638810296540/work/dist
freetype-py @ file:///home/conda/feedstock_root/build_artifacts/freetype-py_1650983368720/work
gast==0.4.0
greenlet @ file:///home/conda/feedstock_root/build_artifacts/greenlet_1702072428820/work
grpcio==1.60.0
h5py==3.10.0
html5lib==1.1
idna @ file:///home/conda/feedstock_root/build_artifacts/idna_1701026962277/work
immutabledict==2.0.0
importlib-metadata==6.6.0
importlib-resources @ file:///home/conda/feedstock_root/build_artifacts/importlib_resources_1699364556997/work
installer==0.7.0
ipykernel @ file:///home/conda/feedstock_root/build_artifacts/ipykernel_1698244021190/work
ipython @ file:///home/conda/feedstock_root/build_artifacts/ipython_1701831663892/work
ipywidgets @ file:///home/conda/feedstock_root/build_artifacts/ipywidgets_1694607144474/work
isoduration @ file:///home/conda/feedstock_root/build_artifacts/isoduration_1638811571363/work/dist
jaraco.classes==3.2.3
jax==0.3.24
jaxlib @ https://storage.googleapis.com/jax-releases/cuda11/jaxlib-0.3.24+cuda11.cudnn82-cp310-cp310-manylinux2014_x86_64.whl#sha256=e085ba12bed53602af7cd5134de69d04bb9a0b27637658451c4c13d12912d489
jedi @ file:///home/conda/feedstock_root/build_artifacts/jedi_1696326070614/work
jeepney @ file:///home/conda/feedstock_root/build_artifacts/jeepney_1649085214306/work
Jinja2 @ file:///home/conda/feedstock_root/build_artifacts/jinja2_1654302431367/work
jmp==0.0.4
json5 @ file:///home/conda/feedstock_root/build_artifacts/json5_1688248289187/work
jsonpointer @ file:///home/conda/feedstock_root/build_artifacts/jsonpointer_1695397238043/work
jsonschema @ file:///home/conda/feedstock_root/build_artifacts/jsonschema-meta_1700159890288/work
jsonschema-specifications @ file:///home/conda/feedstock_root/build_artifacts/jsonschema-specifications_1701365715051/work
jupyter-events @ file:///home/conda/feedstock_root/build_artifacts/jupyter_events_1699285872613/work
jupyter-lsp @ file:///home/conda/feedstock_root/build_artifacts/jupyter-lsp-meta_1701091994466/work/jupyter-lsp
jupyter_client @ file:///home/conda/feedstock_root/build_artifacts/jupyter_client_1699283905679/work
jupyter_core @ file:///home/conda/feedstock_root/build_artifacts/jupyter_core_1698673647019/work
jupyter_server @ file:///home/conda/feedstock_root/build_artifacts/jupyter_server_1701910789300/work
jupyter_server_terminals @ file:///home/conda/feedstock_root/build_artifacts/jupyter_server_terminals_1702308739765/work
jupyterlab @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_1700340792423/work
jupyterlab-widgets @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_widgets_1694598704522/work
jupyterlab_pygments @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_pygments_1700744013163/work
jupyterlab_server @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_server-split_1700310846957/work
keras==2.12.0
keyring==23.13.1
kiwisolver @ file:///home/conda/feedstock_root/build_artifacts/kiwisolver_1695379902431/work
libclang==16.0.6
lockfile==0.12.2
lxml @ file:///home/conda/feedstock_root/build_artifacts/lxml_1695546650907/work
Markdown==3.5.1
MarkupSafe @ file:///home/conda/feedstock_root/build_artifacts/markupsafe_1695367434228/work
matplotlib @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-suite_1700509477637/work
matplotlib-inline @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-inline_1660814786464/work
mda-xdrlib @ file:///home/conda/feedstock_root/build_artifacts/mda-xdrlib_1693318078463/work
mdtraj @ file:///home/conda/feedstock_root/build_artifacts/mdtraj_1700152478883/work
mistune @ file:///home/conda/feedstock_root/build_artifacts/mistune_1698947099619/work
ml-collections==0.1.1
MMPBSA.py==16.0
more-itertools==9.1.0
msgpack @ file:///home/conda/feedstock_root/build_artifacts/msgpack-python_1700926504817/work
munkres==1.1.4
nbclient @ file:///home/conda/feedstock_root/build_artifacts/nbclient_1684790896106/work
nbconvert @ file:///home/conda/feedstock_root/build_artifacts/nbconvert-meta_1701709198055/work
nbformat @ file:///home/conda/feedstock_root/build_artifacts/nbformat_1690814868471/work
nest-asyncio @ file:///home/conda/feedstock_root/build_artifacts/nest-asyncio_1697083700168/work
networkx @ file:///home/conda/feedstock_root/build_artifacts/networkx_1698504735452/work
notebook @ file:///home/conda/feedstock_root/build_artifacts/notebook_1697550696415/work
notebook_shim @ file:///home/conda/feedstock_root/build_artifacts/notebook-shim_1682360583588/work
numexpr @ file:///home/conda/feedstock_root/build_artifacts/numexpr_1697637000856/work
numpy==1.22.0
oauthlib==3.2.2
openff-amber-ff-ports @ file:///home/conda/feedstock_root/build_artifacts/openff-amber-ff-ports_1699301684704/work
openff-interchange @ file:///home/conda/feedstock_root/build_artifacts/openff-interchange-split_1700225776515/work
openff-models @ file:///home/conda/feedstock_root/build_artifacts/openff-models_1698118159649/work
openff-toolkit @ file:///home/conda/feedstock_root/build_artifacts/openff-toolkit-split_1691514724425/work
openff-units @ file:///home/conda/feedstock_root/build_artifacts/openff-units_1686799508759/work
openff-utilities @ file:///home/conda/feedstock_root/build_artifacts/openff-utilities_1702596199952/work
openforcefields @ file:///home/conda/feedstock_root/build_artifacts/openff-forcefields_1699334150016/work
OpenMM==8.0.0
openmmforcefields @ file:///home/conda/feedstock_root/build_artifacts/openmmforcefields_1686858783680/work
opt-einsum==3.3.0
optax==0.1.4
overrides @ file:///home/conda/feedstock_root/build_artifacts/overrides_1691338815398/work
packaging @ file:///home/conda/feedstock_root/build_artifacts/packaging_1696202382185/work
packmol-memgen==1.2.3rc0
pandas==1.3.5
pandocfilters @ file:///home/conda/feedstock_root/build_artifacts/pandocfilters_1631603243851/work
panedr @ file:///home/conda/feedstock_root/build_artifacts/panedr_1693840395005/work
ParmEd @ file:///home/conda/feedstock_root/build_artifacts/parmed_1698252976997/work
parso @ file:///home/conda/feedstock_root/build_artifacts/parso_1638334955874/work
pbr @ file:///home/conda/feedstock_root/build_artifacts/pbr_1699384704298/work
pdb4amber==22.0
pdbfixer @ file:///home/conda/feedstock_root/build_artifacts/pdbfixer_1631833746479/work
pexpect @ file:///home/conda/feedstock_root/build_artifacts/pexpect_1667297516076/work
pickleshare @ file:///home/conda/feedstock_root/build_artifacts/pickleshare_1602536217715/work
Pillow @ file:///home/conda/feedstock_root/build_artifacts/pillow_1695247203795/work
Pint @ file:///home/conda/feedstock_root/build_artifacts/pint_1683140320592/work
pkginfo==1.9.6
pkgutil_resolve_name @ file:///home/conda/feedstock_root/build_artifacts/pkgutil-resolve-name_1694617248815/work
platformdirs @ file:///home/conda/feedstock_root/build_artifacts/platformdirs_1696272223550/work
ply==3.11
Pmw @ file:///home/conda/feedstock_root/build_artifacts/pmw_1695847125009/work
poetry==1.5.1
poetry-core==1.6.1
poetry-plugin-export==1.4.0
prometheus-client @ file:///home/conda/feedstock_root/build_artifacts/prometheus_client_1700579315247/work
prompt-toolkit @ file:///home/conda/feedstock_root/build_artifacts/prompt-toolkit_1702399386289/work
protobuf==4.25.1
psutil @ file:///home/conda/feedstock_root/build_artifacts/psutil_1695367094274/work
ptyprocess @ file:///home/conda/feedstock_root/build_artifacts/ptyprocess_1609419310487/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl
pure-eval @ file:///home/conda/feedstock_root/build_artifacts/pure_eval_1642875951954/work
py-cpuinfo @ file:///home/conda/feedstock_root/build_artifacts/py-cpuinfo_1666774466606/work
pyasn1==0.5.1
pyasn1-modules==0.3.0
pycairo==1.25.0
pycparser @ file:///home/conda/feedstock_root/build_artifacts/pycparser_1636257122734/work
pydantic @ file:///home/conda/feedstock_root/build_artifacts/pydantic_1700669197061/work
pydantic_core @ file:///home/conda/feedstock_root/build_artifacts/pydantic-core_1700663989698/work
pyedr @ file:///home/conda/feedstock_root/build_artifacts/pyedr_1693834451417/work
Pygments @ file:///home/conda/feedstock_root/build_artifacts/pygments_1700607939962/work
pymol==2.5.0
pyMSMT==22.0
pyparsing @ file:///home/conda/feedstock_root/build_artifacts/pyparsing_1690737849915/work
pyproject_hooks==1.0.0
PyQt5==5.15.9
PyQt5-sip==12.12.2
PySocks @ file:///home/conda/feedstock_root/build_artifacts/pysocks_1661604839144/work
python-constraint==1.4.0
python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/python-dateutil_1626286286081/work
python-json-logger @ file:///home/conda/feedstock_root/build_artifacts/python-json-logger_1677079630776/work
pytraj==2.0.6
pytz @ file:///home/conda/feedstock_root/build_artifacts/pytz_1693930252784/work
PyYAML @ file:///home/conda/feedstock_root/build_artifacts/pyyaml_1695373428874/work
pyzmq @ file:///home/conda/feedstock_root/build_artifacts/pyzmq_1701783169502/work
rapidfuzz @ file:///home/conda/feedstock_root/build_artifacts/rapidfuzz_1698999384006/work
rdkit-pypi==2022.9.5
referencing @ file:///home/conda/feedstock_root/build_artifacts/referencing_1701974441252/work
reportlab @ file:///home/conda/feedstock_root/build_artifacts/reportlab_1702306239088/work
requests @ file:///home/conda/feedstock_root/build_artifacts/requests_1684774241324/work
requests-oauthlib==1.3.1
requests-toolbelt==1.0.0
rfc3339-validator @ file:///home/conda/feedstock_root/build_artifacts/rfc3339-validator_1638811747357/work
rfc3986-validator @ file:///home/conda/feedstock_root/build_artifacts/rfc3986-validator_1598024191506/work
rlPyCairo @ file:///home/conda/feedstock_root/build_artifacts/rlpycairo_1687519531733/work
rpds-py @ file:///home/conda/feedstock_root/build_artifacts/rpds-py_1701307945274/work
rsa==4.9
sander==22.0
scipy==1.7.3
SecretStorage @ file:///home/conda/feedstock_root/build_artifacts/secretstorage_1695551734488/work
Send2Trash @ file:///home/conda/feedstock_root/build_artifacts/send2trash_1682601222253/work
shellingham==1.5.0.post1
sip @ file:///home/conda/feedstock_root/build_artifacts/sip_1697300428978/work
six @ file:///home/conda/feedstock_root/build_artifacts/six_1620240208055/work
smirnoff99frosst @ file:///home/conda/feedstock_root/build_artifacts/smirnoff99frosst_1610626268593/work
sniffio @ file:///home/conda/feedstock_root/build_artifacts/sniffio_1662051266223/work
soupsieve @ file:///home/conda/feedstock_root/build_artifacts/soupsieve_1693929250441/work
SQLAlchemy @ file:///home/conda/feedstock_root/build_artifacts/sqlalchemy_1698950567251/work
stack-data @ file:///home/conda/feedstock_root/build_artifacts/stack_data_1669632077133/work
tables @ file:///home/conda/feedstock_root/build_artifacts/pytables_1687843140272/work
tabulate==0.9.0
tensorboard==2.12.3
tensorboard-data-server==0.7.2
tensorflow==2.12.0
tensorflow-estimator==2.12.0
tensorflow-io-gcs-filesystem==0.34.0
termcolor==2.4.0
terminado @ file:///home/conda/feedstock_root/build_artifacts/terminado_1699810101464/work
tinycss2 @ file:///home/conda/feedstock_root/build_artifacts/tinycss2_1666100256010/work
tinydb @ file:///home/conda/feedstock_root/build_artifacts/tinydb_1686607385119/work
toml @ file:///home/conda/feedstock_root/build_artifacts/toml_1604308577558/work
tomli @ file:///home/conda/feedstock_root/build_artifacts/tomli_1644342247877/work
tomlkit==0.11.8
toolz==0.12.0
tornado @ file:///home/conda/feedstock_root/build_artifacts/tornado_1695373560918/work
tqdm @ file:///home/conda/feedstock_root/build_artifacts/tqdm_1691671248568/work
traitlets @ file:///home/conda/feedstock_root/build_artifacts/traitlets_1701095650114/work
trove-classifiers==2023.5.24
types-python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/types-python-dateutil_1689882883784/work
typing-utils @ file:///home/conda/feedstock_root/build_artifacts/typing_utils_1622899189314/work
typing_extensions @ file:///home/conda/feedstock_root/build_artifacts/typing_extensions_1702176139754/work
tzdata @ file:///home/conda/feedstock_root/build_artifacts/python-tzdata_1680081134351/work
unicodedata2 @ file:///home/conda/feedstock_root/build_artifacts/unicodedata2_1695847980273/work
uri-template @ file:///home/conda/feedstock_root/build_artifacts/uri-template_1688655812972/work/dist
urllib3 @ file:///home/conda/feedstock_root/build_artifacts/urllib3_1699933488691/work
userpath==1.8.0
validators @ file:///home/conda/feedstock_root/build_artifacts/validators_1693659212288/work
virtualenv==20.23.0
wcwidth @ file:///home/conda/feedstock_root/build_artifacts/wcwidth_1700607916581/work
webcolors @ file:///home/conda/feedstock_root/build_artifacts/webcolors_1679900785843/work
webencodings @ file:///home/conda/feedstock_root/build_artifacts/webencodings_1694681268211/work
websocket-client @ file:///home/conda/feedstock_root/build_artifacts/websocket-client_1701630677416/work
Werkzeug==3.0.1
widgetsnbextension @ file:///home/conda/feedstock_root/build_artifacts/widgetsnbextension_1694598693908/work
wrapt==1.14.1
xmltodict @ file:///home/conda/feedstock_root/build_artifacts/xmltodict_1652020822199/work
zipp @ file:///home/conda/feedstock_root/build_artifacts/zipp_1695255097490/work

[YaoYinYing]

Hi, I want to install it on a server that does not allow for conda-mediated installation. Could you provide a requirements.txt file to be compatible with PIP installation?

@Sinsilcobio Hi, I think this fork may help you with PIP installation of Umol. However, model relaxation requires openmm and openff, which can only be accessible from Conda.

[biochristmas]

@YaoYinYing Hi, I installed Umol based on the folk you provided, but encountered the error shown in the screenshot during the test run. Could you please provide some suggestions for resolving this issue? Thank you very much.

[YaoYinYing]

@biochristmas It looks like CUDA and/or CuDNN library are somehow misconfigured. You need to consult your HPC administrator for more details.

[biochristmas]

@YaoYinYing Thank you very much for your advice. I will try to contact the administrator and address the issue.