Very large molecules consume huge amounts of memory #101

Yoshanuikabundi · 2024-04-02T05:28:00Z

I tried to charge a 5177 atom (349 residue) protein with NAGL. It took about fifty minutes before my kernel killed it because it had consumed all 64 GB of memory on my machine. I charged it with the OpenFF Toolkit's Molecule.assign_partial_charges() method.

My understanding is that NAGL should be roughly linear-ish in time and space, and I've successfully charged a 10ish residue peptide in about 250 ms (which was awesome), which means ~50x more atoms lead to ~12000x time. I wonder if there's any low hanging fruit that could be picked to optimize NAGL for large molecules?

Jeff thought it might be related to the combinatorics of computing tautomers - the Toolkit recently changed from by default only producing the top ~10 tautomers to asking for as many as the backend can give.

Code to reproduce the behavior

from openff.toolkit.utils.nagl_wrapper import NAGLToolkitWrapper
from openff.toolkit import Molecule

protein = Molecule.from_smiles(
    "CC[C@H](C)[C@H](NC(=O)CNC(=O)CNC(=O)[C@H](CCC(N)=O)NC(=O)[C@H](CCC(N)=O)NC(=O)[C@H](CC(=O)[O-])NC(=O)[C@H](CC(=O)[O-])NC(=O)[C@H](CCCNC(N)=[NH2+])NC(=O)CNC(=O)[C@H](CS)NC(=O)[C@@H](NC(=O)[C@H](CCCNC(N)=[NH2+])NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H](NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)[C@H](CC(C)C)NC(=O)CNC(=O)[C@H](CCCNC(N)=[NH2+])NC(=O)[C@H](CCC(=O)[O-])NC(=O)[C@@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H](NC(=O)[C@@H]1CCCN1C(=O)[C@H](CC(N)=O)NC(=O)[C@@H](NC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@@H]1CCCN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H](CCC(=O)[O-])NC(=O)[C@H](CC(C)C)NC(=O)[C@@H](NC(=O)CNC(=O)[C@H](CC(N)=O)NC(=O)[C@H](CCC(=O)[O-])NC(=O)[C@H](C)NC(=O)[C@H](Cc1ccc(O)cc1)NC(=O)[C@@H](NC(=O)[C@H](CCC(=O)[O-])NC(=O)[C@H](CO)NC(=O)[C@H](C)NC(=O)[C@@H]1CCCN1C(=O)[C@@H](NC(=O)[C@H](CO)NC(=O)[C@@H](NC(=O)CNC(=O)[C@H](CO)NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](Cc1cnc[nH]1)NC(=O)CNC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](CCCC[NH3+])NC(=O)[C@@H](NC(=O)CNC(=O)[C@H](CC(=O)[O-])NC(=O)[C@H](C)NC(=O)[C@@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](CCCC[NH3+])NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](C)NC(=O)[C@@H](NC(=O)[C@H](CO)NC(=O)[C@@H](NC(=O)CNC(=O)[C@H](CCC(N)=O)NC(=O)[C@H](CCCC[NH3+])NC(=O)[C@@H]1CCCN1C(=O)[C@H](CC(=O)[O-])NC(=O)[C@H](CO)NC(=O)[C@@H](NC(=O)[C@H](CC(=O)[O-])NC(=O)[C@H](CC(=O)[O-])NC(=O)CNC(=O)[C@H](CC(C)C)NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H](CCCC[NH3+])NC(=O)[C@@H](NC(=O)[C@H](CCC(N)=O)NC(=O)[C@H](CCC(=O)[O-])NC(=O)CNC(=O)[C@H](CC(N)=O)NC(=O)[C@@H](NC(=O)CNC(=O)CNC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@H](CC(N)=O)NC(=O)[C@@H](NC(=O)[C@H](CC(=O)[O-])NC(=O)[C@H](CCCC[NH3+])NC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@H](CCC(N)=O)NC(=O)[C@H](CCC(=O)[O-])NC(=O)[C@H](C)NC(=O)CNC(=O)[C@H](CCCC[NH3+])NC(=O)[C@H](CCC(N)=O)NC(=O)[C@@H](NC(=O)[C@H](CCC(N)=O)NC(=O)[C@H](C)NC(=O)CNC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@H](CC(N)=O)NC(=O)[C@@H]1CCCN1C(=O)CNC(=O)[C@@H](NC(=O)[C@H](CC(C)C)NC(=O)[C@@H]1CCCN1C(=O)[C@H](C)NC(=O)CNC(=O)[C@@H](NC(=O)[C@H](C)NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H](CC(=O)[O-])NC(=O)[C@@H]([NH3+])CCSC)C(C)C)C(C)C)[C@@H](C)CC)C(C)C)[C@@H](C)O)[C@@H](C)CC)[C@@H](C)CC)[C@@H](C)CC)[C@@H](C)CC)[C@@H](C)CC)C(C)C)C(C)C)[C@@H](C)CC)C(C)C)C(C)C)C(C)C)C(C)C)C(C)C)C(C)C)[C@@H](C)CC)C(C)C)[C@@H](C)CC)[C@@H](C)CC)[C@@H](C)O)[C@@H](C)O)C(C)C)[C@@H](C)O)[C@@H](C)O)[C@@H](C)O)C(=O)N[C@@H](C)C(=O)NCC(=O)N[C@@H](CCCC[NH3+])C(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C)C(=O)N[C@@H](CC(=O)[O-])C(=O)N[C@@H](Cc1c[nH]cn1)C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](CCCC[NH3+])C(=O)N[C@@H](CC(=O)[O-])C(=O)N[C@@H](C)C(=O)N[C@@H](CCCC[NH3+])C(=O)N[C@H](C(=O)N[C@@H](C)C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@@H](Cc1cnc[nH]1)C(=O)N[C@@H](CC(=O)[O-])C(=O)N[C@@H](CCCC[NH3+])C(=O)N[C@H](C(=O)N1CCC[C@H]1C(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)NCC(=O)N[C@@H](CCC(N)=O)C(=O)NCC(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C)C(=O)N[C@@H](CC(=O)[O-])C(=O)N[C@@H](CCC(=O)[O-])C(=O)N[C@H](C(=O)N[C@@H](CCCC[NH3+])C(=O)N[C@@H](CCCC[NH3+])C(=O)N[C@@H](C)C(=O)N[C@@H](C)C(=O)N[C@@H](CC(N)=O)C(=O)N[C@@H](C)C(=O)N[C@@H](C)C(=O)NCC(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@@H](CCC(=O)[O-])C(=O)N[C@H](C(=O)N[C@@H](CCSC)C(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@@H](CCC(=O)[O-])C(=O)NCC(=O)N[C@H](C(=O)N[C@@H](CC(N)=O)C(=O)N[C@H](C(=O)N[C@@H](CS[C@H]1CC(=O)N(c2ccc3c(c2)C(=O)OC32c3ccc(O)cc3Oc3cc(O)ccc32)C1=O)C(=O)N[C@@H](CC(=O)[O-])C(=O)N[C@@H](CCCC[NH3+])C(=O)N[C@@H](CC(=O)[O-])C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](CO)C(=O)N[C@@H](C)C(=O)N[C@@H](CC(C)C)C(=O)N[C@H](C(=O)N[C@@H](CO)C(=O)N[C@@H](CCCC[NH3+])C(=O)N[C@@H](CCSC)C(=O)N[C@@H](CCCC[NH3+])C(=O)N[C@@H](CCC(=O)[O-])C(=O)N[C@@H](C)C(=O)NCC(=O)N[C@H](C(=O)N[C@@H](CO)C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(=O)NCC(=O)NCC(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](Cc1c[nH]cn1)C(=O)N[C@H](C(=O)N[C@@H](CCC(=O)[O-])C(=O)N[C@@H](C)C(=O)NCC(=O)N[C@@H](CC(C)C)C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@@H](CCCNC(N)=[NH2+])C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@@H](C)C(=O)N[C@@H](C)C(=O)N[C@@H](CC(=O)[O-])C(=O)N[C@@H](CCC(N)=O)C(=O)NCC(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](CCCC[NH3+])C(=O)N[C@@H](C)C(=O)N[C@@H](CCCC[NH3+])C(=O)N[C@@H](CC(C)C)C(=O)N[C@H](C(=O)N[C@@H](CO)C(=O)NCC(=O)N[C@@H](CC(=O)[O-])C(=O)NCC(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@@H](CO)C(=O)N[C@@H](CC(N)=O)C(=O)N[C@@H](CCC(=O)[O-])C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C)C(=O)N[C@@H](CO)C(=O)N[C@H](C(=O)N[C@@H](C)C(=O)NCC(=O)N[C@@H](CC(=O)[O-])C(=O)N[C@@H](C)C(=O)N[C@H](C(=O)N[C@@H](CCC(=O)[O-])C(=O)NCC(=O)N[C@H](C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](CC(N)=O)C(=O)N[C@H](C(=O)N[C@@H](Cc1ccccc1)C(=O)NCC(=O)N1CCC[C@H]1C(=O)N[C@@H](CC(=O)[O-])C(=O)N1CCC[C@H]1C(=O)N[C@H](C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](CCCNC(N)=[NH2+])C(=O)N1CCC[C@H]1C(=O)N[C@@H](CCC(=O)[O-])C(=O)N[C@@H](CC(N)=O)C(=O)N[C@@H](CCCC[NH3+])C(=O)N[C@@H](CCC(=O)[O-])C(=O)N[C@@H](CC(C)C)C(=O)N[C@H](C(=O)N[C@@H](CCC(=O)[O-])C(=O)N[C@@H](CCCC[NH3+])C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](CCCC[NH3+])C(=O)N[C@@H](C)C(=O)N[C@@H](C)C(=O)NCC(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](CC(N)=O)C(=O)N1CCC[C@H]1C(=O)N[C@@H](CCC(=O)[O-])C(=O)N[C@@H](C)C(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@H](C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@@H](CO)C(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@@H](C)C(=O)N[C@@H](C)C(=O)N[C@@H](CCSC)C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@@H](C)C(=O)N[C@H](C(=O)N[C@@H](C)C(=O)NCC(=O)N[C@@H](C)C(=O)N[C@@H](C)C(=O)N[C@@H](CCCC[NH3+])C(=O)N[C@@H](C)C(=O)N[C@@H](C)C(=O)NCC(=O)N[C@@H](CO)C(=O)N[C@H](C(=O)N[C@@H](CCC(=O)[O-])C(=O)N1CCC[C@H]1C(=O)N[C@@H](CCC(=O)[O-])C(=O)N[C@@H](CCCC[NH3+])C(=O)N[C@H](C(=O)N[C@@H](C)C(=O)N[C@@H](CCC(=O)[O-])C(=O)N[C@@H](C)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](CCCC[NH3+])C(=O)N[C@@H](CCCC[NH3+])C(=O)NCC(=O)N[C@@H](CO)C(=O)N[C@@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)N[C@H](C(=O)N[C@@H](C)C(=O)N[C@@H](CC(C)C)C(=O)NCC(=O)N[C@@H](CCC(=O)[O-])C(=O)N[C@H](C(=O)N[C@@H](CO)C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](CC(=O)[O-])C(=O)N[C@@H](CCC(=O)[O-])C(=O)N[C@@H](CCCC[NH3+])C(=O)NCC(=O)N[C@@H](CC(=O)[O-])C(=O)N1CCC[C@H]1C(=O)N[C@@H](CCCC[NH3+])C(=O)N[C@@H](CC(C)C)C(=O)N1CCC[C@H]1C(=O)NCC(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@H](C(=O)N[C@@H](CCSC)C(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@@H](CCC(=O)[O-])C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(=O)N[C@@H](CCCC[NH3+])C(=O)N[C@@H](CCCC[NH3+])C(=O)NCC(=O)N1CCC[C@H]1C(=O)N[C@@H](CC(=O)[O-])C(=O)NCC(=O)N[C@@H](CCCC[NH3+])C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@H](C(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@H](C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@@H](CCC(N)=O)C(=O)NC)[C@@H](C)CC)[C@@H](C)O)C(C)C)[C@@H](C)CC)[C@@H](C)O)C(C)C)C(C)C)[C@@H](C)CC)[C@@H](C)O)C(C)C)[C@@H](C)O)[C@@H](C)O)[C@@H](C)O)C(C)C)[C@@H](C)CC)C(C)C)[C@@H](C)CC)C(C)C)[C@@H](C)CC)[C@@H](C)CC)[C@@H](C)O)[C@@H](C)CC)[C@@H](C)CC)C(C)C)[C@@H](C)CC)C(C)C)C(C)C)C(C)C)[C@@H](C)O)C(C)C)[C@@H](C)O)[C@@H](C)O)[C@@H](C)CC)[C@@H](C)CC)C(C)C"
)

protein.assign_partial_charges(
    "openff-gnn-am1bcc-0.1.0-rc.1.pt", toolkit_registry=NAGLToolkitWrapper()
)

(SMILES is my favorite format for sharing proteins)

Current environment

Which version are you using? 0.3.6
Which version of Python (python -V)? 3.10.14
Which operating system? Arch Linux
What is the output of pip list?

pip list

Package                   Version
------------------------- ----------------------------
absl-py                   2.1.0
aiohttp                   3.9.3
aiosignal                 1.3.1
AmberLite                 22.0
AmberUtils                21.0
annotated-types           0.6.0
anyio                     4.3.0
argcomplete               3.2.3
argon2-cffi               23.1.0
argon2-cffi-bindings      21.2.0
arrow                     1.3.0
ase                       3.22.1
asttokens                 2.4.1
astunparse                1.6.3
async-lru                 2.0.4
async-timeout             4.0.3
attrs                     23.2.0
Babel                     2.14.0
basis-set-exchange        0.9.1
beautifulsoup4            4.12.3
biopython                 1.83
black                     24.3.0
bleach                    6.1.0
blinker                   1.7.0
Brotli                    1.0.9
bson                      0.5.9
cached-property           1.5.2
cachetools                5.3.3
cattrs                    23.2.3
certifi                   2024.2.2
cffi                      1.16.0
cftime                    1.6.3
chardet                   5.2.0
charset-normalizer        3.3.2
chemper                   1.0.0
click                     8.1.7
click-option-group        0.5.6
cloudpickle               3.0.0
colorama                  0.4.6
comm                      0.2.2
contourpy                 1.2.0
cryptography              42.0.5
cycler                    0.12.1
Cython                    3.0.9
cytoolz                   0.12.3
dask                      2024.3.1
dask-jobqueue             0.8.5
debugpy                   1.8.1
decorator                 5.1.1
defusedxml                0.7.1
dgl                       1.1.2
distributed               2024.3.1
dockstring                0.3.2
docstring-to-markdown     0.15
entrypoints               0.4
exceptiongroup            1.2.0
executing                 2.0.1
f90wrap                   0.2.13
fasteners                 0.17.3
fastjsonschema            2.19.1
filelock                  3.13.3
Flask                     3.0.2
flatbuffers               24.3.25
fonttools                 4.50.0
fqdn                      1.5.1
freetype-py               2.3.0
frozenlist                1.4.1
fsspec                    2024.3.1
gast                      0.4.0
gitdb                     4.0.11
GitPython                 3.1.42
gmpy2                     2.1.2
google-auth               2.29.0
google-auth-oauthlib      0.4.6
google-pasta              0.2.0
greenlet                  3.0.3
GridDataFormats           1.0.2
grpcio                    1.51.1
gsd                       3.2.1
h11                       0.14.0
h2                        4.1.0
h5py                      3.8.0
hpack                     4.0.0
httpcore                  1.0.5
httpx                     0.27.0
hyperframe                6.0.1
idna                      3.6
importlib_metadata        7.1.0
importlib_resources       6.4.0
injector                  0.20.1
ipykernel                 6.29.3
ipython                   8.22.2
ipywidgets                8.1.2
isoduration               20.11.0
isort                     5.13.2
itsdangerous              2.1.2
jax                       0.4.4
jaxlib                    0.4.3
jedi                      0.19.1
jedi-language-server      0.41.3
Jinja2                    3.1.3
joblib                    1.3.2
json5                     0.9.24
jsonpointer               2.4
jsonschema                4.21.1
jsonschema-specifications 2023.12.1
jupyter_client            8.6.1
jupyter_core              5.7.2
jupyter-events            0.10.0
jupyter-lsp               2.2.4
jupyter_server            2.13.0
jupyter_server_terminals  0.5.3
jupyterlab                4.1.5
jupyterlab_code_formatter 2.2.1
jupyterlab_execute_time   3.1.2
jupyterlab-lsp            5.1.0
jupyterlab_pygments       0.3.0
jupyterlab_server         2.25.4
jupyterlab_widgets        3.0.10
keras                     2.11.0
Keras-Preprocessing       1.1.2
kiwisolver                1.4.5
lammps                    2022.6.23
lightning-utilities       0.11.2
llvmlite                  0.42.0
locket                    1.0.0
lsprotocol                2023.0.1
lxml                      4.9.2
Markdown                  3.6
markdown-it-py            3.0.0
MarkupSafe                2.1.5
matplotlib                3.8.3
matplotlib-inline         0.1.6
mda-xdrlib                0.2.0
MDAnalysis                2.7.0
mdtraj                    1.9.9
mdurl                     0.1.2
mistune                   3.0.2
mmcif-pdbx                2.0.1
MMPBSA.py                 16.0
mmtf-python               1.1.3
mpiplus                   0+untagged.38.gfd8a5aa.dirty
mpmath                    1.3.0
mrcfile                   1.5.0
msgpack                   1.0.7
multidict                 6.0.5
munkres                   1.1.4
mypy-extensions           1.0.0
nbclient                  0.10.0
nbconvert                 7.16.3
nbformat                  5.10.3
nest_asyncio              1.6.0
netCDF4                   1.6.2
networkx                  3.2.1
nglview                   3.1.2
nose                      1.3.7
notebook                  7.1.2
notebook_shim             0.2.4
numba                     0.59.1
numexpr                   2.9.0
numpy                     1.26.4
oauthlib                  3.2.2
openff-amber-ff-ports     0+untagged.32.g809f411.dirty
openff-interchange        0.3.24
openff-models             0.1.2
openff-nagl               0.3.6
openff-nagl-models        0.1.2
openff-qcsubmit           0.50.3
openff-recharge           0.5.2
openff-toolkit            0.15.2
openff-units              0.2.2
openff-utilities          0.1.12
openforcefields           2024.3.0
OpenMM                    8.1.1
openmmforcefields         0.12.0
openmmtools               0.23.1
opt-einsum                3.3.0
overrides                 7.7.0
packaging                 24.0
packmol-memgen            1.2.3rc0
pandas                    2.2.1
pandocfilters             1.5.0
panedr                    0.8.0
ParmEd                    3.4.4
parso                     0.8.3
partd                     1.4.1
pathspec                  0.12.1
patsy                     0.5.6
pdb2pqr                   3.6.1
pdb4amber                 22.0
pdbfixer                  1.9.0
pexpect                   4.9.0
pickleshare               0.7.5
pid                       3.0.4
Pillow                    9.4.0
Pint                      0.23
pip                       24.0
pkgutil_resolve_name      1.3.10
platformdirs              4.2.0
plotly                    5.19.0
prometheus_client         0.20.0
prompt-toolkit            3.0.42
propka                    3.5.1
protobuf                  4.21.12
psutil                    5.9.8
ptyprocess                0.7.0
pure-eval                 0.2.2
py-cpuinfo                9.0.0
pyarrow                   11.0.0
pyasn1                    0.5.1
pyasn1-modules            0.3.0
pycairo                   1.25.0
pycparser                 2.21
pydantic                  2.6.4
pydantic_core             2.16.3
pyedr                     0.8.0
pygls                     1.3.1
Pygments                  2.17.2
PyJWT                     2.8.0
pymbar                    4.0.3
pyMSMT                    22.0
pyOpenSSL                 24.0.0
pyparsing                 3.1.2
PySocks                   1.7.1
python-constraint         1.4.0
python-dateutil           2.9.0
python-json-logger        2.0.7
pytng                     0.0.0
pytorch-lightning         2.2.1
pytraj                    2.0.6
pytz                      2024.1
pyu2f                     0.1.5
PyYAML                    6.0.1
pyzmq                     25.1.2
qcelemental               0.27.1
qcengine                  0.29.0
qcportal                  0.53
quippy                    NOT-A-GIT-REPOSITORY
referencing               0.34.0
regex                     2023.12.25
reportlab                 4.1.0
requests                  2.31.0
requests-oauthlib         2.0.0
rfc3339-validator         0.1.4
rfc3986-validator         0.1.1
rich                      13.7.1
rlPyCairo                 0.2.0
rpds-py                   0.18.0
rsa                       4.9
sander                    22.0
scikit-learn              1.4.1.post1
scipy                     1.12.0
seaborn                   0.13.2
Send2Trash                1.8.2
setuptools                69.2.0
six                       1.16.0
smirnoff99frosst          0+unknown
smmap                     5.0.0
sniffio                   1.3.1
sortedcontainers          2.4.0
soupsieve                 2.5
SQLAlchemy                2.0.29
stack-data                0.6.2
statsmodels               0.14.1
sympy                     1.12
tables                    3.7.0
tabulate                  0.9.0
tblib                     3.0.0
tenacity                  8.2.3
tensorboard               2.11.2
tensorboard-data-server   0.6.1
tensorboard-plugin-wit    1.8.1
tensorflow                2.11.0
tensorflow-estimator      2.11.0
termcolor                 2.4.0
terminado                 0.18.1
threadpoolctl             3.4.0
tidynamics                1.1.2
tinycss2                  1.2.1
tinydb                    4.8.0
tomli                     2.0.1
toolz                     0.12.1
torch                     2.0.0
torchmetrics              1.3.2
tornado                   6.4
tqdm                      4.66.2
traitlets                 5.14.2
transitions               0.8.11
types-python-dateutil     2.9.0.20240316
typing_extensions         4.10.0
typing-utils              0.1.0
tzdata                    2024.1
unicodedata2              15.1.0
Unidecode                 1.3.8
uri-template              1.3.0
urllib3                   2.2.1
validators                0.24.0
wcwidth                   0.2.13
webcolors                 1.13
webencodings              0.5.1
websocket-client          1.7.0
Werkzeug                  3.0.1
wheel                     0.43.0
widgetsnbextension        4.0.10
wrapt                     1.16.0
xmltodict                 0.13.0
xtb                       22.1
yarl                      1.9.4
zict                      3.0.0
zipp                      3.17.0
zstandard                 0.22.0

If you use conda, what is the output of conda list?

micromamba list

List of packages in environment: "/home/joshmitchell/Documents/openff/2024_workshops/.soap/test"

Name Version ──────────── _libgcc_mutex 0.1 _openmp_mutex 4.5 absl-py 2.1.0 aiohttp 3.9.3 aiosignal 1.3.1 ambertools 22.0 annotated-types 0.6.0 anyio 4.3.0 argcomplete 3.2.3 argon2-cffi 23.1.0 argon2-cffi-bindings 21.2.0 arpack 3.7.0 arrow 1.3.0 arrow-cpp 11.0.0 ase 3.22.1 asttokens 2.4.1 astunparse 1.6.3 async-lru 2.0.4 async-timeout 4.0.3 attrs 23.2.0 aws-c-auth 0.6.24 aws-c-cal 0.5.20 aws-c-common 0.8.11 aws-c-compression 0.2.16 aws-c-event-stream 0.2.18 aws-c-http 0.7.4 aws-c-io 0.13.17 aws-c-mqtt 0.8.6 aws-c-s3 0.2.4 aws-c-sdkutils 0.1.7 aws-checksums 0.1.14 aws-crt-cpp 0.19.7 aws-sdk-cpp 1.10.57 babel 2.14.0 basis_set_exchange 0.9.1 beautifulsoup4 4.12.3 binutils_impl_linux-64 2.40 binutils_linux-64 2.40 biopython 1.83 black 24.3.0 bleach 6.1.0 blinker 1.7.0 blosc 1.21.5 boost 1.74.0 boost-cpp 1.74.0 brotli 1.0.9 brotli-bin 1.0.9 brotli-python 1.0.9 bson 0.5.9 bzip2 1.0.8 c-ares 1.27.0 ca-certificates 2024.2.2 cached-property 1.5.2 cached_property 1.5.2 cachetools 5.3.3 cairo 1.16.0 cattrs 23.2.3 certifi 2024.2.2 cffi 1.16.0 cftime 1.6.3 chardet 5.2.0 charset-normalizer 3.3.2 chemper 1.0.1 click 8.1.7 click-option-group 0.5.6 cloudpickle 3.0.0 cmake 3.29.0 colorama 0.4.6 comm 0.2.2 contourpy 1.2.0 cryptography 42.0.5 cudatoolkit 11.8.0 curl 8.7.1 cycler 0.12.1 cython 3.0.9 cytoolz 0.12.3 dask-core 2024.3.1 dask-jobqueue 0.8.5 debugpy 1.8.1 decorator 5.1.1 defusedxml 0.7.1 dgl 1.1.2 distributed 2024.3.1 dockstring 0.3.2 docstring-to-markdown 0.15 entrypoints 0.4 exceptiongroup 1.2.0 executing 2.0.1 expat 2.6.2 f90wrap 0.2.13 fasteners 0.17.3 fftw 3.3.10 filelock 3.13.3 flask 3.0.2 flatbuffers 22.12.06 font-ttf-dejavu-sans-mono 2.37 font-ttf-inconsolata 3.000 font-ttf-source-code-pro 2.038 font-ttf-ubuntu 0.83 fontconfig 2.14.2 fonts-conda-ecosystem 1 fonts-conda-forge 1 fonttools 4.50.0 fqdn 1.5.1 freetype 2.12.1 freetype-py 2.3.0 frozenlist 1.4.1 fsspec 2024.3.1 gast 0.4.0 gawk 5.3.0 gcc_impl_linux-64 11.4.0 gcc_linux-64 11.4.0 gettext 0.21.1 gflags 2.2.2 gfortran_impl_linux-64 11.4.0 gfortran_linux-64 11.4.0 giflib 5.2.1 gitdb 4.0.11 gitpython 3.1.42 glog 0.6.0 gmp 6.3.0 gmpy2 2.1.2 google-auth 2.29.0 google-auth-oauthlib 0.4.6 google-pasta 0.2.0 greenlet 3.0.3 griddataformats 1.0.2 gromacs 2023.1 grpcio 1.51.1 gsd 3.2.1 gsl 2.7 gxx_impl_linux-64 11.4.0 gxx_linux-64 11.4.0 h11 0.14.0 h2 4.1.0 h5py 3.8.0 hdf4 4.2.15 hdf5 1.12.2 hpack 4.0.0 httpcore 1.0.5 httpx 0.27.0 hyperframe 6.0.1 icu 70.1 idna 3.6 importlib-metadata 7.1.0 importlib_metadata 7.1.0 importlib_resources 6.4.0 ipykernel 6.29.3 ipython 8.22.2 ipywidgets 8.1.2 isoduration 20.11.0 isort 5.13.2 itsdangerous 2.1.2 jax 0.4.4 jaxlib 0.4.3 jedi 0.19.1 jedi-language-server 0.41.3 jinja2 3.1.3 joblib 1.3.2 jpeg 9e json5 0.9.24 jsonpointer 2.4 jsonschema 4.21.1 jsonschema-specifications 2023.12.1 jsonschema-with-format-nongpl 4.21.1 jupyter-lsp 2.2.4 jupyter_client 8.6.1 jupyter_core 5.7.2 jupyter_events 0.10.0 jupyter_server 2.13.0 jupyter_server_terminals 0.5.3 jupyterlab 4.1.5 jupyterlab-lsp 5.1.0 jupyterlab_code_formatter 2.2.1 jupyterlab_execute_time 3.1.2 jupyterlab_pygments 0.3.0 jupyterlab_server 2.25.4 jupyterlab_widgets 3.0.10 keras 2.11.0 keras-preprocessing 1.1.2 kernel-headers_linux-64 2.6.32 keyutils 1.6.1 kim-api 2.3.0 kiwisolver 1.4.5 krb5 1.21.2 lammps 2022.06.23 lcms2 2.15 ld_impl_linux-64 2.40 lerc 4.0.0 libabseil 20220623.0 libaec 1.1.3 libarrow 11.0.0 libblas 3.9.0 libbrotlicommon 1.0.9 libbrotlidec 1.0.9 libbrotlienc 1.0.9 libcblas 3.9.0 libcrc32c 1.1.2 libcurl 8.7.1 libdeflate 1.17 libedit libev 4.33 libevent 2.1.10 libexpat 2.6.2 libffi 3.4.2 libgcc-devel_linux-64 11.4.0 libgcc-ng 13.2.0 libgfortran-ng 13.2.0 libgfortran5 13.2.0 libglib 2.80.0 libgomp 13.2.0 libgoogle-cloud 2.7.0 libgrpc 1.51.1 libhwloc 2.9.1 libiconv 1.17 libidn2 2.3.7 liblapack 3.9.0 liblapacke 3.9.0 libllvm14 14.0.6 libnetcdf 4.8.1 libnghttp2 1.58.0 libnsl 2.0.1 libopenblas 0.3.26 libpng 1.6.43 libprotobuf 3.21.12 libsanitizer 11.4.0 libsodium 1.0.18 libsqlite 3.45.2 libssh2 1.11.0 libstdcxx-devel_linux-64 11.4.0 libstdcxx-ng 13.2.0 libthrift 0.18.0 libtiff 4.5.0 libunistring 0.9.10 libutf8proc 2.8.0 libuuid 2.38.1 libuv 1.48.0 libwebp-base 1.3.2 libxcb 1.13 libxcrypt 4.4.36 libxml2 2.10.3 libxslt 1.1.37 libzip 1.10.1 libzlib 1.2.13 lightning-utilities 0.11.2 llvmlite 0.42.0 locket 1.0.0 lsprotocol 2023.0.1 lxml 4.9.2 lz4-c 1.9.4 lzo 2.10 make 4.3 markdown 3.6 markdown-it-py 3.0.0 markupsafe 2.1.5 matplotlib-base 3.8.3 matplotlib-inline 0.1.6 mctc-lib 0.3.1 mda-xdrlib 0.2.0 mdanalysis 2.7.0 mdtraj 1.9.9 mdurl 0.1.2 metis 5.1.1 mistune 3.0.2 mlip 1.0 mmcif_pdbx 2.0.1 mmtf-python 1.1.3 mpc 1.3.1 mpfr 4.2.1 mpi 1.0 mpich 4.2.0 mpiplus v0.0.2 mpmath 1.3.0 mrcfile 1.5.0 msgpack-python 1.0.7 multidict 6.0.5 munkres 1.1.4 mypy_extensions 1.0.0 n2p2 2.1.4 nbclient 0.10.0 nbconvert 7.16.3 nbconvert-core 7.16.3 nbconvert-pandoc 7.16.3 nbformat 5.10.3 ncurses nest-asyncio 1.6.0 netcdf-fortran 4.6.0 netcdf4 1.6.2 networkx 3.2.1 nglview 3.1.2 nomkl 1.0 nose 1.3.7 notebook 7.1.2 notebook-shim 0.2.4 numba 0.59.1 numexpr 2.9.0 numpy 1.26.4 oauthlib 3.2.2 ocl-icd 2.3.2 ocl-icd-system 1.0.0 openbabel 3.1.1 openff-amber-ff-ports 0.0.4 openff-forcefields 2024.03.0 openff-interchange 0.3.24 openff-interchange-base 0.3.24 openff-models 0.1.2 openff-nagl 0.3.6 openff-nagl-base 0.3.6 openff-nagl-models 0.1.2 openff-qcsubmit 0.50.3 openff-recharge 0.5.2 openff-toolkit 0.15.2 openff-toolkit-base 0.15.2 openff-toolkit-examples 0.15.2 openff-units 0.2.2 openff-utilities 0.1.12 openjpeg 2.5.0 openmm 8.1.1 openmmforcefields 0.12.0 openmmtools 0.23.1 openssl 3.2.1 opt_einsum 3.3.0 orc 1.8.2 overrides 7.7.0 packaging 24.0 packmol 20.010 pandas 2.2.1 pandoc 3.1.12.3 pandocfilters 1.5.0 panedr 0.8.0 parmed 3.4.4 parquet-cpp 1.5.1 parso 0.8.3 partd 1.4.1 pathspec 0.12.1 patsy 0.5.6 pcre2 10.43 pdb2pqr 3.6.1 pdbfixer 1.9 perl 5.32.1 pexpect 4.9.0 pickleshare 0.7.5 pillow 9.4.0 pint 0.23 pip 24.0 pixman 0.43.2 pkg-config 0.29.2 pkgutil-resolve-name 1.3.10 platformdirs 4.2.0 plotly 5.19.0 plumed 2.9.0 prometheus_client 0.20.0 prompt-toolkit 3.0.42 propka 3.5.1 protobuf 4.21.12 psutil 5.9.8 pthread-stubs 0.4 ptyprocess 0.7.0 pure_eval 0.2.2 py-cpuinfo 9.0.0 pyarrow 11.0.0 pyasn1 0.5.1 pyasn1-modules 0.3.0 pycairo 1.25.0 pycparser 2.21 pydantic 2.6.4 pydantic-core 2.16.3 pyedr 0.8.0 pygls 1.3.1 pygments 2.17.2 pyjwt 2.8.0 pymbar 4.0.3 pymbar-core 4.0.3 pyopenssl 24.0.0 pyparsing 3.1.2 pysocks 1.7.1 pytables 3.7.0 python 3.10.14 python-constraint 1.4.0 python-dateutil 2.9.0 python-fastjsonschema 2.19.1 python-flatbuffers 24.3.25 python-json-logger 2.0.7 python-tzdata 2024.1 python_abi 3.10 pytng 0.3.1 pytorch 2.0.0 pytorch-lightning 2.2.1 pytz 2024.1 pyu2f 0.1.5 pyyaml 6.0.1 pyzmq 25.1.2 qcelemental 0.27.1 qcengine 0.29.0 qcportal 0.53 quippy 0.0.1 rdkit 2022.03.5 re2 2023.02.01 readline 8.2 referencing 0.34.0 regex 2023.12.25 reportlab 4.1.0 requests 2.31.0 requests-oauthlib 2.0.0 rfc3339-validator 0.1.4 rfc3986-validator 0.1.1 rhash 1.4.4 rich 13.7.1 rlpycairo 0.2.0 rpds-py 0.18.0 rsa 4.9 s2n 1.3.37 scikit-learn scipy 1.12.0 seaborn 0.13.2 seaborn-base 0.13.2 send2trash 1.8.2 setuptools 69.2.0 six 1.16.0 sleef 3.5.1 smirnoff99frosst 1.1.0 smmap 5.0.0 snappy 1.1.10 sniffio 1.3.1 sortedcontainers 2.4.0 soupsieve 2.5 sqlalchemy 2.0.29 sqlite 3.45.2 stack_data 0.6.2 statsmodels 0.14.1 sympy 1.12 sysroot_linux-64 2.12 tabulate 0.9.0 tblib 3.0.0 tenacity 8.2.3 tensorboard 2.11.2 tensorboard-data-server 0.6.1 tensorboard-plugin-wit 1.8.1 tensorflow 2.11.0 tensorflow-base 2.11.0 tensorflow-estimator 2.11.0 termcolor 2.4.0 terminado 0.18.1 threadpoolctl 3.4.0 tidynamics 1.1.2 tinycss2 1.2.1 tinydb 4.8.0 tk 8.6.13 tomli 2.0.1 toolz 0.12.1 torchmetrics 1.3.2 tornado 6.4 tqdm 4.66.2 traitlets 5.14.2 types-python-dateutil typing-extensions 4.10.0 typing_extensions 4.10.0 typing_utils 0.1.0 tzdata 2024a unicodedata2 15.1.0 unidecode 1.3.8 uri-template 1.3.0 urllib3 2.2.1 validators 0.24.0 voro 0.4.6 wcwidth 0.2.13 webcolors 1.13 webencodings 0.5.1 websocket-client 1.7.0 werkzeug 3.0.1 wget 1.21.4 wheel 0.43.0 widgetsnbextension 4.0.10 wrapt 1.16.0 xmltodict 0.13.0 xorg-kbproto 1.0.7 xorg-libice 1.0.10 xorg-libsm 1.2.3 xorg-libx11 1.8.4 xorg-libxau 1.0.11 xorg-libxdmcp 1.1.3 xorg-libxext 1.3.4 xorg-libxrender 0.9.10 xorg-libxt 1.3.0 xorg-renderproto 0.11.1 xorg-xextproto 7.3.0 xorg-xproto 7.0.31 xtb 6.5.1 xtb-python 22.1 xz 5.2.6 yaml 0.2.5 yarl 1.9.4 zeromq 4.3.5 zict 3.0.0 zipp 3.17.0 zlib 1.2.13 zstandard 0.22.0 zstd 1.5.5 Build Channel
───────────────────────────────────────────────────────────────────────────────
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The text was updated successfully, but these errors were encountered:

lilyminium · 2024-04-02T06:20:56Z

My first thought is usually resonance structures but I'll do a proper profile of what's going on. Thanks for the report!

lilyminium · 2024-04-05T06:52:06Z

Ok... I think I've got this consistently down to ~110 seconds with and without DGL, ~1.9 GiB with OpenEye, ~450 MiB with RDKit for reasons I describe in openforcefield/openff-toolkit#1855. It's still not linear scaling, and undoubtedly there's a lot of optimization that could be further done -- most of the additional time takes place in the resonance enumeration that still makes a lot of use of networkx and suboptimal data structures. I'll get this merged and released ASAP though so NAGL is remotely usable for larger molecules.

Yoshanuikabundi · 2024-04-05T10:25:10Z

THAT'S AWESOME!!! 110 seconds is EXTREMELY usable. This is going to make the NCAA vignette such a hard flex.

lilyminium · 2024-04-05T10:45:30Z

GitHub was down for a little but just made a release that will hopefully show up on conda soon!

This was referenced Apr 5, 2024

oemol.GetConfs() consuming large amount of memory even when no conformers are present openforcefield/openff-toolkit#1855

Open

Improve explosions in memory and time during inference #102

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lilyminium closed this as completed in #102 Apr 5, 2024

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Very large molecules consume huge amounts of memory #101

Very large molecules consume huge amounts of memory #101

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lilyminium commented Apr 5, 2024 •

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Yoshanuikabundi commented Apr 5, 2024

lilyminium commented Apr 5, 2024

Very large molecules consume huge amounts of memory #101

Very large molecules consume huge amounts of memory #101

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Yoshanuikabundi commented Apr 2, 2024

Code to reproduce the behavior

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lilyminium commented Apr 2, 2024

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lilyminium commented Apr 5, 2024 •

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