Open mikemhenry opened 2 years ago
mikemhenry
commented
2 years ago I will also get this merged in https://github.com/conda-forge/espaloma-feedstock/pull/2 so that we don't have users install espaloma from conda-forge with an incompatible openff toolkit.
LeifSeute
commented
2 years ago Another incompatibility with the new openff toolkit version appears upon loading the datasets provided in the examples, e.g. https://espaloma.wangyq.net/experiments/mm_fitting_small .
This caused by the introduction of hierarchy schemes ( https://docs.openforcefield.org/projects/toolkit/en/latest/releasehistory.html#atom-metadata-and-hierarchy-schemes-for-iterating-over-residues-chains-etc ). The espaloma.graphs.graph.Graph.load method throws a key error when trying to call Molecule.from_json(). This can be solved by recreating the datasets using the new openff toolkit or by manually adding the key 'hierarchy_schemes' to the json files.
bchodkowski-vir
commented
1 year ago What is the best way for me to fix this error:
AttributeError: Neither Quantity object nor its magnitude (0.0) has attribute 'value_in_unit'I am running this example python code:
import os
import torch
import espaloma as esp
# grab pretrained model
if not os.path.exists("espaloma_model.pt"):
os.system("wget http://data.wangyq.net/espaloma_model.pt")
# define or load a molecule of interest via the Open Force Field toolkit
from openff.toolkit.topology import Molecule
molecule = Molecule.from_smiles("CN1C=NC2=C1C(=O)N(C(=O)N2C)C")
# create an Espaloma Graph object to represent the molecule of interest
molecule_graph = esp.Graph(molecule)The above error occurs on the last line (esp.Graph(molecule)).
What I've done:
# download espaloma v0.2.4 from
# https://github.com/choderalab/espaloma/archive/refs/tags/0.2.4.tar.gz
tar -xvzf espaloma-0.2.4.tar.gz
mv espaloma-0.2.4 espaloma
cd espaloma
# create espaloma-perses virtual environment
conda env create -n espaloma-perses \
-f ./scripts/perses-benchmark/espaloma-perses.yaml \
| tee conda_activate_espaloma-perses.log
# activate virtual environment
conda activate espaloma-perses
# install
python setup.py install | tee python_setup_install.log
which -a python
# /opt/conda/envs/espaloma-perses/bin/python
python --version
# Python 3.10.6
which -a ipython
# /opt/conda/envs/espaloma-perses/bin/ipython
# /usr/local/bin/ipython
which -a pip
# /opt/conda/envs/espaloma-perses/bin/pip
# /usr/local/bin/pipPATH is defined as:
(espaloma-perses) $ echo $PATH | perl -pe 's/:/\n/g' | cat -n
1 .
2 /home/ubuntu/bin
3 /home/ubuntu/.local/bin
4 /home/linuxbrew/.linuxbrew/bin
5 /home/linuxbrew/.linuxbrew/sbin
6 /opt/conda/envs/espaloma-perses/bin
7 /opt/conda/condabin
8 /opt/amazon/openmpi/bin
9 /opt/amazon/efa/bin
10 /usr/local/cuda/bin
11 /usr/local/sbin
12 /usr/local/bin
13 /usr/sbin
14 /usr/bin
15 /sbin
16 /bin
17 /usr/games
18 /usr/local/games
19 /snap/binConda environment:
(espaloma-perses) $ conda list
# packages in environment at /opt/conda/envs/espaloma-perses:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_kmp_llvm conda-forge
alabaster 0.7.12 py_0 conda-forge
alsa-lib 1.2.7.2 h166bdaf_0 conda-forge
amberlite 22.0 pypi_0 pypi
ambertools 22.0 py310h3aec49d_3 conda-forge
amberutils 21.0 pypi_0 pypi
argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 pypi_0 pypi
arpack 3.7.0 hdefa2d7_2 conda-forge
arrow-cpp 9.0.0 py310h9c91e85_7_cpu conda-forge
arsenic 0.2.1 py310hff52083_0 conda-forge
asttokens 2.0.8 pyhd8ed1ab_0 conda-forge
astunparse 1.6.3 pyhd8ed1ab_0 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
attrs 22.1.0 pyh71513ae_1 conda-forge
aws-c-cal 0.5.11 h95a6274_0 conda-forge
aws-c-common 0.6.2 h7f98852_0 conda-forge
aws-c-event-stream 0.2.7 h3541f99_13 conda-forge
aws-c-io 0.10.5 hfb6a706_0 conda-forge
aws-checksums 0.1.11 ha31a3da_7 conda-forge
aws-sdk-cpp 1.8.186 hb4091e7_3 conda-forge
babel 2.10.3 pyhd8ed1ab_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.11.1 pyha770c72_0 conda-forge
bleach 5.0.1 pyhd8ed1ab_0 conda-forge
blosc 1.21.1 h83bc5f7_3 conda-forge
bokeh 2.4.3 pyhd8ed1ab_3 conda-forge
boost 1.74.0 py310h7c3ba0c_5 conda-forge
boost-cpp 1.74.0 h75c5d50_8 conda-forge
brotli 1.0.9 h166bdaf_7 conda-forge
brotli-bin 1.0.9 h166bdaf_7 conda-forge
brotlipy 0.7.0 pypi_0 pypi
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2022.9.24 ha878542_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 5.2.0 pyhd8ed1ab_0 conda-forge
cairo 1.16.0 ha61ee94_1014 conda-forge
certifi 2022.9.24 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 pypi_0 pypi
cftime 1.6.2 pypi_0 pypi
charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge
click 8.1.3 pypi_0 pypi
cloudpickle 2.2.0 pyhd8ed1ab_0 conda-forge
codecov 2.1.11 pyhd3deb0d_0 conda-forge
colorama 0.4.5 pyhd8ed1ab_0 conda-forge
contourpy 1.0.5 pypi_0 pypi
coverage 6.5.0 pypi_0 pypi
cryptography 38.0.2 pypi_0 pypi
cudatoolkit 11.7.0 hd8887f6_10 conda-forge
cudnn 8.4.1.50 hed8a83a_0 conda-forge
curl 7.85.0 h7bff187_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cython 0.29.32 pypi_0 pypi
cytoolz 0.12.0 pypi_0 pypi
dask 2022.10.0 pyhd8ed1ab_2 conda-forge
dask-core 2022.10.0 pyhd8ed1ab_1 conda-forge
dask-jobqueue 0.8.1 pyhd8ed1ab_0 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
debugpy 1.6.3 pypi_0 pypi
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
dgl 0.9.1 pypi_0 pypi
dicttoxml 1.7.4 pyhd8ed1ab_2 conda-forge
distributed 2022.10.0 pyhd8ed1ab_2 conda-forge
docutils 0.17.1 pypi_0 pypi
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
espaloma 0.2.2 pypi_0 pypi
executing 1.1.1 pyhd8ed1ab_0 conda-forge
expat 2.4.9 h27087fc_0 conda-forge
fftw 3.3.10 nompi_hf0379b8_105 conda-forge
fire 0.4.0 pyh44b312d_0 conda-forge
flit-core 3.7.1 pyhd8ed1ab_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.14.0 hc2a2eb6_1 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.37.4 pypi_0 pypi
freetype 2.12.1 hca18f0e_0 conda-forge
fsspec 2022.10.0 pyhd8ed1ab_0 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
gflags 2.2.2 he1b5a44_1004 conda-forge
glib 2.74.0 h6239696_0 conda-forge
glib-tools 2.74.0 h6239696_0 conda-forge
glog 0.6.0 h6f12383_0 conda-forge
greenlet 1.1.3 pypi_0 pypi
grpc-cpp 1.47.1 h05bd8bd_6 conda-forge
gst-plugins-base 1.20.3 h57caac4_2 conda-forge
gstreamer 1.20.3 hd4edc92_2 conda-forge
h5py 3.7.0 pypi_0 pypi
hdf4 4.2.15 h9772cbc_4 conda-forge
hdf5 1.12.2 nompi_h2386368_100 conda-forge
heapdict 1.0.1 py_0 conda-forge
icu 70.1 h27087fc_0 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
imagesize 1.4.1 pyhd8ed1ab_0 conda-forge
importlib-metadata 4.11.4 pypi_0 pypi
importlib_resources 5.10.0 pyhd8ed1ab_0 conda-forge
iniconfig 1.1.1 pyh9f0ad1d_0 conda-forge
ipykernel 6.16.1 pyh210e3f2_0 conda-forge
ipython 8.5.0 pyh41d4057_1 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 8.0.2 pyhd8ed1ab_1 conda-forge
jack 1.9.21 h2a1e645_0 conda-forge
jedi 0.18.1 pyhd8ed1ab_2 conda-forge
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
joblib 1.2.0 pyhd8ed1ab_0 conda-forge
jpeg 9e h166bdaf_2 conda-forge
jsonschema 4.16.0 pyhd8ed1ab_0 conda-forge
jupyter-core 4.11.1 pypi_0 pypi
jupyter_client 7.3.4 pyhd8ed1ab_0 conda-forge
jupyter_core 4.11.1 py310hff52083_0 conda-forge
jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge
jupyterlab_widgets 3.0.3 pyhd8ed1ab_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.4 pypi_0 pypi
krb5 1.19.3 h3790be6_0 conda-forge
lame 3.100 h166bdaf_1003 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.39 hc81fddc_0 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libabseil 20220623.0 cxx17_h48a1fff_4 conda-forge
libblas 3.9.0 16_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h166bdaf_7 conda-forge
libbrotlidec 1.0.9 h166bdaf_7 conda-forge
libbrotlienc 1.0.9 h166bdaf_7 conda-forge
libcap 2.66 ha37c62d_0 conda-forge
libcblas 3.9.0 16_linux64_openblas conda-forge
libclang 14.0.6 default_h2e3cab8_0 conda-forge
libclang13 14.0.6 default_h3a83d3e_0 conda-forge
libcrc32c 1.1.2 h9c3ff4c_0 conda-forge
libcups 2.3.3 h3e49a29_2 conda-forge
libcurl 7.85.0 h7bff187_0 conda-forge
libdb 6.2.32 h9c3ff4c_0 conda-forge
libdeflate 1.14 h166bdaf_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libevent 2.1.10 h9b69904_4 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libflac 1.4.1 h27087fc_0 conda-forge
libgcc-ng 12.2.0 h65d4601_18 conda-forge
libgfortran-ng 12.2.0 h69a702a_18 conda-forge
libgfortran5 12.2.0 h337968e_18 conda-forge
libglib 2.74.0 h7a41b64_0 conda-forge
libgomp 12.2.0 h65d4601_18 conda-forge
libgoogle-cloud 2.2.0 h838d150_1 conda-forge
libiconv 1.17 h166bdaf_0 conda-forge
liblapack 3.9.0 16_linux64_openblas conda-forge
libllvm11 11.1.0 he0ac6c6_4 conda-forge
libllvm14 14.0.6 he0ac6c6_0 conda-forge
libnetcdf 4.8.1 nompi_h21705cb_104 conda-forge
libnghttp2 1.47.0 hdcd2b5c_1 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpng 1.6.38 h753d276_0 conda-forge
libpq 14.5 hd77ab85_0 conda-forge
libprotobuf 3.21.8 h6239696_0 conda-forge
libsndfile 1.1.0 h27087fc_0 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libsqlite 3.39.4 h753d276_0 conda-forge
libssh2 1.10.0 haa6b8db_3 conda-forge
libstdcxx-ng 12.2.0 h46fd767_18 conda-forge
libthrift 0.16.0 h491838f_2 conda-forge
libtiff 4.4.0 h55922b4_4 conda-forge
libtool 2.4.6 h9c3ff4c_1008 conda-forge
libudev1 249 h166bdaf_4 conda-forge
libutf8proc 2.7.0 h7f98852_0 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp-base 1.2.4 h166bdaf_0 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxkbcommon 1.0.3 he3ba5ed_0 conda-forge
libxml2 2.10.3 h7463322_0 conda-forge
libxslt 1.1.35 h8affb1d_0 conda-forge
libzip 1.9.2 hc869a4a_1 conda-forge
libzlib 1.2.13 h166bdaf_4 conda-forge
llvm-openmp 14.0.4 he0ac6c6_0 conda-forge
llvmlite 0.39.1 pypi_0 pypi
locket 1.0.0 pyhd8ed1ab_0 conda-forge
lxml 4.9.1 pypi_0 pypi
lz4 4.0.0 pypi_0 pypi
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
lzo 2.10 h516909a_1000 conda-forge
magma 2.5.4 hc72dce7_3 conda-forge
markupsafe 2.1.1 pypi_0 pypi
matplotlib 3.6.1 pypi_0 pypi
matplotlib-base 3.6.1 py310h8d5ebf3_0 conda-forge
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
mdtraj 1.9.7 pypi_0 pypi
mistune 2.0.4 pyhd8ed1ab_0 conda-forge
mkl 2022.1.0 h84fe81f_915 conda-forge
mmpbsa-py 16.0 pypi_0 pypi
mpg123 1.30.2 h27087fc_1 conda-forge
mpiplus v0.0.1 pyhd8ed1ab_1003 conda-forge
msgpack 1.0.4 pypi_0 pypi
msgpack-python 1.0.4 py310hbf28c38_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mysql-common 8.0.31 haf5c9bc_0 conda-forge
mysql-libs 8.0.31 h28c427c_0 conda-forge
nbclient 0.7.0 pyhd8ed1ab_0 conda-forge
nbconvert 7.2.2 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.2.2 pyhd8ed1ab_0 conda-forge
nbconvert-pandoc 7.2.2 pyhd8ed1ab_0 conda-forge
nbformat 5.7.0 pyhd8ed1ab_0 conda-forge
nccl 2.14.3.1 h0800d71_0 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
nest-asyncio 1.5.6 pyhd8ed1ab_0 conda-forge
netcdf-fortran 4.6.0 nompi_hc402ea5_101 conda-forge
netcdf4 1.6.1 pypi_0 pypi
networkx 2.8.7 pyhd8ed1ab_0 conda-forge
nglview 3.0.3 pyh8a188c0_0 conda-forge
ninja 1.11.0 h924138e_0 conda-forge
nose 1.3.7 py_1006 conda-forge
nose-timer 1.0.1 pyhd8ed1ab_0 conda-forge
notebook 6.4.12 pyha770c72_0 conda-forge
nspr 4.32 h9c3ff4c_1 conda-forge
nss 3.78 h2350873_0 conda-forge
numba 0.56.3 pypi_0 pypi
numexpr 2.7.3 pypi_0 pypi
numpy 1.23.4 pypi_0 pypi
numpydoc 1.5.0 pyhd8ed1ab_0 conda-forge
ocl-icd 2.3.1 h7f98852_0 conda-forge
ocl-icd-system 1.0.0 1 conda-forge
openeye-toolkits 2022.1.1 py310_0 openeye
openeye-toolkits-python3-linux-x64 2022.1.1 pypi_0 pypi
openff-amber-ff-ports 0.0.3 pyh6c4a22f_0 conda-forge
openff-arsenic 0+untagged.10.g0234410.dirty pypi_0 pypi
openff-forcefields 2.0.0 pyh6c4a22f_0 conda-forge
openff-interchange 0.2.2 pyhd8ed1ab_0 conda-forge
openff-interchange-base 0.2.2 pyhd8ed1ab_0 conda-forge
openff-toolkit 0.11.2 pyhd8ed1ab_1 conda-forge
openff-toolkit-base 0.11.2 pyhd8ed1ab_1 conda-forge
openff-units 0.1.8 pyh1a96a4e_0 conda-forge
openff-utilities 0.1.7 pyh1a96a4e_0 conda-forge
openjpeg 2.5.0 h7d73246_1 conda-forge
openmm 7.7.0 pypi_0 pypi
openmmforcefields 0.11.2+1.g9309ba8 pypi_0 pypi
openmmtools 0.21.5 pyhd8ed1ab_0 conda-forge
openmoltools 0.8.8 pyhd8ed1ab_1 conda-forge
openssl 1.1.1q h166bdaf_1 conda-forge
orc 1.8.0 h09e0d61_0 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
packmol 20.010 h86c2bf4_0 conda-forge
packmol-memgen 1.2.3rc0 pypi_0 pypi
pandas 1.5.1 pypi_0 pypi
pandoc 2.19.2 ha770c72_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
panedr 0.5.2 py_0 conda-forge
parmed 3.4.3 pypi_0 pypi
parquet-cpp 1.5.1 2 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
partd 1.3.0 pyhd8ed1ab_0 conda-forge
patsy 0.5.3 pyhd8ed1ab_0 conda-forge
pbr 5.11.0 pyhd8ed1ab_0 conda-forge
pcre2 10.37 hc3806b6_1 conda-forge
pdb4amber 22.0 pypi_0 pypi
pdbfixer 1.8.1 pyh6c4a22f_0 conda-forge
perl 5.32.1 2_h7f98852_perl5 conda-forge
perses 0.10.1 pyh8a188c0_0 conda-forge
pexpect 4.8.0 pyh9f0ad1d_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 9.2.0 pypi_0 pypi
pint 0.19.2 pyhd8ed1ab_0 conda-forge
pip 22.3 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge
plotly 5.10.0 pyhd8ed1ab_0 conda-forge
pluggy 1.0.0 pypi_0 pypi
ply 3.11 py_1 conda-forge
prometheus_client 0.15.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.31 pyha770c72_0 conda-forge
psutil 5.9.3 pypi_0 pypi
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pulseaudio 14.0 habe0971_10 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
py 1.11.0 pyh6c4a22f_0 conda-forge
pyarrow 9.0.0 pypi_0 pypi
pycairo 1.21.0 pypi_0 pypi
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pydantic 1.10.2 pypi_0 pypi
pygments 2.13.0 pyhd8ed1ab_0 conda-forge
pymbar 3.0.5 pypi_0 pypi
pymsmt 22.0 pypi_0 pypi
pyopenssl 22.1.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge
pyqt 5.15.7 py310h29803b5_1 conda-forge
pyqt5 5.15.7 pypi_0 pypi
pyqt5-sip 12.11.0 pypi_0 pypi
pyrsistent 0.18.1 pypi_0 pypi
pysocks 1.7.1 pyha2e5f31_6 conda-forge
pytables 3.7.0 py310hb60b9b2_2 conda-forge
pytest 7.1.3 pypi_0 pypi
pytest-cov 4.0.0 pyhd8ed1ab_0 conda-forge
python 3.10.6 h582c2e5_0_cpython conda-forge
python-constraint 1.4.0 py_0 conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.16.2 pyhd8ed1ab_0 conda-forge
python_abi 3.10 2_cp310 conda-forge
pytorch 1.12.1 cuda112py310he33e0d6_201 conda-forge
pytraj 2.0.6 pypi_0 pypi
pytz 2022.5 pyhd8ed1ab_0 conda-forge
pyyaml 6.0 pypi_0 pypi
pyzmq 24.0.1 pypi_0 pypi
qcelemental 0.25.0 pyhd8ed1ab_0 conda-forge
qcportal 0.15.8 pyhd8ed1ab_0 conda-forge
qt-main 5.15.6 hc525480_0 conda-forge
rdkit 2022.03.5 py310h1c297d8_0 conda-forge
re2 2022.06.01 h27087fc_0 conda-forge
readline 8.1.2 h0f457ee_0 conda-forge
reportlab 3.5.68 pypi_0 pypi
requests 2.28.1 pyhd8ed1ab_1 conda-forge
s2n 1.0.10 h9b69904_0 conda-forge
sander 22.0 pypi_0 pypi
scikit-learn 1.1.2 pypi_0 pypi
scipy 1.9.3 pypi_0 pypi
seaborn 0.12.0 hd8ed1ab_0 conda-forge
seaborn-base 0.12.0 pyhd8ed1ab_0 conda-forge
send2trash 1.8.0 pyhd8ed1ab_0 conda-forge
setuptools 65.5.0 pyhd8ed1ab_0 conda-forge
sip 6.7.2 pypi_0 pypi
six 1.16.0 pyh6c4a22f_0 conda-forge
sleef 3.5.1 h9b69904_2 conda-forge
smirnoff99frosst 1.1.0 pyh44b312d_0 conda-forge
snappy 1.1.9 hbd366e4_1 conda-forge
snowballstemmer 2.2.0 pyhd8ed1ab_0 conda-forge
sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge
sphinx 5.3.0 pyhd8ed1ab_0 conda-forge
sphinx_rtd_theme 1.0.0 pyhd8ed1ab_0 conda-forge
sphinxcontrib-applehelp 1.0.2 py_0 conda-forge
sphinxcontrib-devhelp 1.0.2 py_0 conda-forge
sphinxcontrib-htmlhelp 2.0.0 pyhd8ed1ab_0 conda-forge
sphinxcontrib-jsmath 1.0.1 py_0 conda-forge
sphinxcontrib-qthelp 1.0.3 py_0 conda-forge
sphinxcontrib-serializinghtml 1.1.5 pyhd8ed1ab_2 conda-forge
sqlalchemy 1.4.42 pypi_0 pypi
sqlite 3.39.4 h4ff8645_0 conda-forge
stack_data 0.5.1 pyhd8ed1ab_0 conda-forge
statsmodels 0.13.2 pypi_0 pypi
tables 3.7.0 pypi_0 pypi
tbb 2021.6.0 h924138e_0 conda-forge
tblib 1.7.0 pyhd8ed1ab_0 conda-forge
tenacity 8.1.0 pyhd8ed1ab_0 conda-forge
termcolor 2.0.1 pyhd8ed1ab_1 conda-forge
terminado 0.16.0 pyh41d4057_0 conda-forge
threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge
tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge
tinydb 4.7.0 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
toolz 0.12.0 pyhd8ed1ab_0 conda-forge
torch 1.12.1.post201 pypi_0 pypi
tornado 6.1 pypi_0 pypi
tqdm 4.64.1 pyhd8ed1ab_0 conda-forge
traitlets 5.5.0 pyhd8ed1ab_0 conda-forge
typing-extensions 4.4.0 hd8ed1ab_0 conda-forge
typing_extensions 4.4.0 pyha770c72_0 conda-forge
tzdata 2022e h191b570_0 conda-forge
unicodedata2 14.0.0 pypi_0 pypi
urllib3 1.26.11 pyhd8ed1ab_0 conda-forge
validators 0.18.2 pyhd3deb0d_0 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
webencodings 0.5.1 py_1 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
widgetsnbextension 4.0.3 pyhd8ed1ab_0 conda-forge
xcb-util 0.4.0 h166bdaf_0 conda-forge
xcb-util-image 0.4.0 h166bdaf_0 conda-forge
xcb-util-keysyms 0.4.0 h166bdaf_0 conda-forge
xcb-util-renderutil 0.3.9 h166bdaf_0 conda-forge
xcb-util-wm 0.4.1 h166bdaf_0 conda-forge
xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.2 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-libxt 1.2.1 h7f98852_2 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zeromq 4.3.4 h9c3ff4c_1 conda-forge
zict 2.2.0 pyhd8ed1ab_0 conda-forge
zipp 3.9.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 h166bdaf_4 conda-forge
zstd 1.5.2 h6239696_4 conda-forgeAny help would be appreciated. We are testing espaloma using a time-limited trial license from OpenEye. Thank you.
diogomart
commented
1 year ago Hi, this worked for me:
conda install openff-toolkit=0.10.6 -c conda-forge
jchodera
commented
1 year ago @bchodkowski-vir : Sorry about this---we haven't had a chance to update the repo for the latest openff-toolkit release, which adopted a new unit-handling standard that will serve everyone better in the long run.
For now, you'll have to downgrade the openff-toolkit to 0.10 as suggested by @diogomart in https://github.com/choderalab/espaloma/issues/130#issuecomment-1287207255
jchodera
commented
1 year ago @mikemhenry : We may need your help to identify how to update to the new unit-handling framework!
bchodkowski-vir
commented
1 year ago For posterity in case anyone else ends up here:
I had to downgrade:
python to 3.9openff to 0.10 conda list | egrep -i 'openff|^python\s+'
openff-forcefields 2.0.0 pyh6c4a22f_0 conda-forge
openff-toolkit 0.10.6 pyhd8ed1ab_0 conda-forge
openff-toolkit-base 0.10.6 pyhd8ed1ab_0 conda-forge
openff-units 0.1.8 pyh1a96a4e_0 conda-forge
openff-utilities 0.1.7 pyh1a96a4e_0 conda-forge
python 3.9.13 h9a8a25e_0_cpython conda-forgewhen i created the virtual environment from the espaloma-perses.yaml file:
conda env remove --name espaloma-perses
conda env create -n espaloma-perses \
-f ./scripts/perses-benchmark/espaloma-perses.yamlby default i got python3.10.6.
when i tried to uninstall openff-toolkit it got this weird error:
conda uninstall openff-toolkit
Collecting package metadata (repodata.json): done
Solving environment: failed
ResolvePackageNotFound:
- python=3.1i read somewhere that python3.10 was wonky so i defined python3.9 when creating the venv:
conda env create -n espaloma-perses \
python=3.9 \
-f ./scripts/perses-benchmark/espaloma-perses.yamlthis did not work bc python is listed in the .yaml file's dependencies; the resulting venv still had python3.10.6.
i manually updated the .yaml file:
diff espaloma-perses_ba.yaml ./scripts/perses-benchmark/espaloma-perses.yaml
10,11c10
< # ba: added version=3.9
< - python=3.9
---
> - python
18,19c17
< # ba: added version=0.10.6
< - openff-toolkit=0.10.6
---
> - openff-toolkitcreating the venv with this edited .yaml file fixed the openff issues.
thanks!
jchodera
commented
1 year ago Thanks so much for the detailed report, @bchodkowski-vir!
@yuanqing-wang : Let's pin these versions in our environment.yaml files for now.
mikemhenry
commented
1 year ago Ah, I did fix this issue with the conda-forge package, but not for the environment.yaml files in this repository. Sorry about that!
Right now CI is failing due to the new openff toolkit using a different package for units. The openff-unit package provides a way to support both using openmm.units and openff.units. For now in PR #129 I will just pin to the older toolkit, but we should target the new toolkit in the next release.