Fragmentation within bespokefit taking longer than in openff-fragmenter #390
Description
Description
I am attempting to generate parameters for the molecule with smiles "c1cc(c(c(c1)Cl)C(=O)Nc1ccnc(c1)NC(=O)C)Cl". When running the BespokeExecutor, it stalls during fragmentation (its been running for multiple hours). When I attempt to fragment with WBOFragmenter() in isolation, it takes about 6 mins. If I run with the PfizerFragmenter(), the fragmentation in bespokefit succeeds. The code I ran in a jupyter notebook for each scenario is given below.
Code ran for fragmentation using openff-fragmenter
from openff.toolkit.topology import Molecule
molecule = Molecule.from_smiles("c1cc(c(c(c1)Cl)C(=O)Nc1ccnc(c1)NC(=O)C)Cl")
from openff.fragmenter.fragment import WBOFragmenter
frag_engine = WBOFragmenter()
# Export the engine's settings directly to JSON
frag_engine.json()
result = frag_engine.fragment(molecule)
result.json()
Code ran for bespokefit
from openff.bespokefit.executor import BespokeExecutor, BespokeWorkerConfig
from openff.bespokefit.workflows import BespokeWorkflowFactory
from openff.qcsubmit.common_structures import QCSpec
new_factory = BespokeWorkflowFactory(
initial_force_field="openff-2.2.0.offxml",
default_qc_specs=[
QCSpec(
method="gfn2xtb",
program="xtb",
basis=None
)
],
)
new_factory.fragmentation_engine = WBOFragmenter()
from openff.bespokefit.executor import BespokeExecutor, BespokeWorkerConfig
from openff.bespokefit.executor.client import BespokeFitClient, Settings
# create a client to interface with the executor
settings = Settings()
client = BespokeFitClient(settings=settings)
with BespokeExecutor(
n_fragmenter_workers = 1,
n_optimizer_workers = 1,
n_qc_compute_workers = 2,
qc_compute_worker_config=BespokeWorkerConfig(n_cores=1)
) as executor:
# Submit our workflow to the executor
task_id = client.submit_optimization(input_schema=workflow_schema)
# Wait until the executor is done
output = client.wait_until_complete(task_id)
if output.status == "success":
# Save the resulting force field to an OFFXML file
output.bespoke_force_field.to_file("output-ff.offxml")
elif output.status == "errored":
# OR the print the error message if unsuccessful
print(output.error)
Software versions
- BespokeFit was installed using micromamba
Output of conda list
Name Version Build Channel ───────────────────────────────────────────────────────────────────────────────────────────────── _openmp_mutex 4.5 3_kmp_llvm conda-forge ambertools 24.8 cuda_None_nompi_py312h3fa95ad_100 conda-forge amqp 5.2.0 pyhd8ed1ab_2 conda-forge anyio 4.9.0 pyh29332c3_0 conda-forge argcomplete 3.6.1 pyhd8ed1ab_0 conda-forge argon2-cffi 23.1.0 pyhd8ed1ab_1 conda-forge argon2-cffi-bindings 21.2.0 py312h66e93f0_5 conda-forge arpack 3.9.1 nompi_hf03ea27_102 conda-forge arrow 1.3.0 pyhd8ed1ab_1 conda-forge asttokens 3.0.0 pyhd8ed1ab_1 conda-forge async-lru 2.0.5 pyh29332c3_0 conda-forge async-timeout 5.0.1 pyhd8ed1ab_1 conda-forge attrs 25.3.0 pyh71513ae_0 conda-forge babel 2.17.0 pyhd8ed1ab_0 conda-forge backports.zoneinfo 0.2.1 py312h7900ff3_9 conda-forge basis_set_exchange 0.11 pyhd8ed1ab_0 conda-forge beautifulsoup4 4.13.3 pyha770c72_0 conda-forge billiard 4.2.1 py312h66e93f0_0 conda-forge bleach 6.2.0 pyh29332c3_4 conda-forge bleach-with-css 6.2.0 h82add2a_4 conda-forge blosc 1.21.6 he440d0b_1 conda-forge boto3 1.37.25 pyhd8ed1ab_0 conda-forge botocore 1.37.25 pyge310_1234567_0 conda-forge brotli 1.1.0 hb9d3cd8_2 conda-forge brotli-bin 1.1.0 hb9d3cd8_2 conda-forge brotli-python 1.1.0 py312h2ec8cdc_2 conda-forge bson 0.5.10 pyhd8ed1ab_0 conda-forge bzip2 1.0.8 h4bc722e_7 conda-forge c-ares 1.34.4 hb9d3cd8_0 conda-forge c-blosc2 2.17.1 h3122c55_0 conda-forge ca-certificates 2025.1.31 hbcca054_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cachetools 5.5.2 pyhd8ed1ab_0 conda-forge cairo 1.18.4 h3394656_0 conda-forge celery 5.4.0 pyhd8ed1ab_2 conda-forge certifi 2025.1.31 pyhd8ed1ab_0 conda-forge cffi 1.17.1 py312h06ac9bb_0 conda-forge chardet 5.2.0 pyhd8ed1ab_3 conda-forge charset-normalizer 3.4.1 pyhd8ed1ab_0 conda-forge chemper 1.0.1 pyhd8ed1ab_0 conda-forge click 8.1.8 pyh707e725_0 conda-forge click-didyoumean 0.3.1 pyhd8ed1ab_1 conda-forge click-option-group 0.5.6 pyhd8ed1ab_0 conda-forge click-plugins 1.1.1 pyhd8ed1ab_1 conda-forge click-repl 0.3.0 pyhd8ed1ab_0 conda-forge colorama 0.4.6 pyhd8ed1ab_1 conda-forge comm 0.2.2 pyhd8ed1ab_1 conda-forge contourpy 1.3.1 py312h68727a3_0 conda-forge cpython 3.12.9 py312hd8ed1ab_1 conda-forge cudatoolkit 11.8.0 h4ba93d1_13 conda-forge cycler 0.12.1 pyhd8ed1ab_1 conda-forge debugpy 1.8.13 py312h2ec8cdc_0 conda-forge decorator 5.2.1 pyhd8ed1ab_0 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge dftd4 3.7.0 hc15f34f_3 conda-forge dnspython 2.7.0 pyhff2d567_1 conda-forge email-validator 2.2.0 pyhd8ed1ab_1 conda-forge email_validator 2.2.0 hd8ed1ab_1 conda-forge exceptiongroup 1.2.2 pyhd8ed1ab_1 conda-forge executing 2.1.0 pyhd8ed1ab_1 conda-forge fastapi 0.115.12 pyh29332c3_0 conda-forge fastapi-cli 0.0.7 pyhd8ed1ab_0 conda-forge fftw 3.3.10 nompi_hf1063bd_110 conda-forge filelock 3.18.0 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 h77eed37_3 conda-forge fontconfig 2.15.0 h7e30c49_1 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fonttools 4.56.0 py312h178313f_0 conda-forge forcebalance 1.9.6 py312h3eaf749_2 conda-forge fqdn 1.5.1 pyhd8ed1ab_1 conda-forge freetype 2.13.3 h48d6fc4_0 conda-forge freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge fsspec 2025.3.2 pyhd8ed1ab_0 conda-forge future 1.0.0 pyhd8ed1ab_2 conda-forge geometric 1.1 pyhd8ed1ab_1 conda-forge gmp 6.3.0 hac33072_2 conda-forge gmpy2 2.1.5 py312h7201bc8_3 conda-forge greenlet 3.1.1 py312h2ec8cdc_1 conda-forge h11 0.14.0 pyhd8ed1ab_1 conda-forge h2 4.2.0 pyhd8ed1ab_0 conda-forge h5py 3.13.0 nompi_py312hedeef09_100 conda-forge hdf4 4.2.15 h2a13503_7 conda-forge hdf5 1.14.3 nompi_h2d575fe_109 conda-forge hpack 4.1.0 pyhd8ed1ab_0 conda-forge httpcore 1.0.7 pyh29332c3_1 conda-forge httptools 0.6.4 py312h66e93f0_0 conda-forge httpx 0.28.1 pyhd8ed1ab_0 conda-forge hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge icu 75.1 he02047a_0 conda-forge idna 3.10 pyhd8ed1ab_1 conda-forge importlib-metadata 8.6.1 pyha770c72_0 conda-forge importlib_resources 6.5.2 pyhd8ed1ab_0 conda-forge ipykernel 6.29.5 pyh3099207_0 conda-forge ipython 9.0.2 pyhfb0248b_0 conda-forge ipython_pygments_lexers 1.1.1 pyhd8ed1ab_0 conda-forge ipywidgets 8.1.5 pyhd8ed1ab_1 conda-forge isoduration 20.11.0 pyhd8ed1ab_1 conda-forge jedi 0.19.2 pyhd8ed1ab_1 conda-forge jinja2 3.1.6 pyhd8ed1ab_0 conda-forge jmespath 1.0.1 pyhd8ed1ab_1 conda-forge joblib 1.4.2 pyhd8ed1ab_1 conda-forge json5 0.11.0 pyhd8ed1ab_0 conda-forge jsonpointer 3.0.0 py312h7900ff3_1 conda-forge jsonschema 4.23.0 pyhd8ed1ab_1 conda-forge jsonschema-specifications 2024.10.1 pyhd8ed1ab_1 conda-forge jsonschema-with-format-nongpl 4.23.0 hd8ed1ab_1 conda-forge jupyter-lsp 2.2.5 pyhd8ed1ab_1 conda-forge jupyter_client 8.6.3 pyhd8ed1ab_1 conda-forge jupyter_core 5.7.2 pyh31011fe_1 conda-forge jupyter_events 0.12.0 pyh29332c3_0 conda-forge jupyter_server 2.15.0 pyhd8ed1ab_0 conda-forge jupyter_server_terminals 0.5.3 pyhd8ed1ab_1 conda-forge jupyterlab 4.3.6 pyhd8ed1ab_0 conda-forge jupyterlab_pygments 0.3.0 pyhd8ed1ab_2 conda-forge jupyterlab_server 2.27.3 pyhd8ed1ab_1 conda-forge jupyterlab_widgets 3.0.13 pyhd8ed1ab_1 conda-forge kernel-headers_linux-64 3.10.0 he073ed8_18 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.8 py312h84d6215_0 conda-forge kombu 5.4.1 py312h7900ff3_0 conda-forge krb5 1.21.3 h659f571_0 conda-forge lark-parser 0.12.0 pyhd8ed1ab_1 conda-forge lcms2 2.17 h717163a_0 conda-forge ld_impl_linux-64 2.43 h712a8e2_4 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libabseil 20250127.1 cxx17_hbbce691_0 conda-forge libaec 1.1.3 h59595ed_0 conda-forge libblas 3.9.0 31_hfdb39a5_mkl conda-forge libboost 1.84.0 h6c02f8c_7 conda-forge libboost-python 1.84.0 py312hc39e661_7 conda-forge libbrotlicommon 1.1.0 hb9d3cd8_2 conda-forge libbrotlidec 1.1.0 hb9d3cd8_2 conda-forge libbrotlienc 1.1.0 hb9d3cd8_2 conda-forge libcblas 3.9.0 31_h372d94f_mkl conda-forge libcurl 8.13.0 h332b0f4_0 conda-forge libdeflate 1.23 h4ddbbb0_0 conda-forge libedit 3.1.20250104 pl5321h7949ede_0 conda-forge libev 4.33 hd590300_2 conda-forge libexpat 2.7.0 h5888daf_0 conda-forge libffi 3.4.6 h2dba641_1 conda-forge libgcc 14.2.0 h767d61c_2 conda-forge libgcc-ng 14.2.0 h69a702a_2 conda-forge libgfortran 14.2.0 h69a702a_2 conda-forge libgfortran-ng 14.2.0 h69a702a_2 conda-forge libgfortran5 14.2.0 hf1ad2bd_2 conda-forge libglib 2.84.0 h2ff4ddf_0 conda-forge libgomp 14.2.0 h767d61c_2 conda-forge libhwloc 2.11.2 default_h0d58e46_1001 conda-forge libiconv 1.18 h4ce23a2_1 conda-forge libjpeg-turbo 3.0.0 hd590300_1 conda-forge liblapack 3.9.0 31_hc41d3b0_mkl conda-forge liblzma 5.6.4 hb9d3cd8_0 conda-forge libnetcdf 4.9.2 nompi_h00e09a9_116 conda-forge libnghttp2 1.64.0 h161d5f1_0 conda-forge libnsl 2.0.1 hd590300_0 conda-forge libpng 1.6.47 h943b412_0 conda-forge libpq 16.8 h87c4ccc_1 conda-forge libprotobuf 5.29.3 h501fc15_0 conda-forge librdkit 2024.03.5 h79cfef2_3 conda-forge libsodium 1.0.20 h4ab18f5_0 conda-forge libsqlite 3.49.1 hee588c1_2 conda-forge libssh2 1.11.1 hf672d98_0 conda-forge libstdcxx 14.2.0 h8f9b012_2 conda-forge libstdcxx-ng 14.2.0 h4852527_2 conda-forge libtiff 4.7.0 hd9ff511_3 conda-forge libtorch 2.6.0 cpu_mkl_hec71012_103 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libuv 1.50.0 hb9d3cd8_0 conda-forge libwebp-base 1.5.0 h851e524_0 conda-forge libxcb 1.17.0 h8a09558_0 conda-forge libxcrypt 4.4.36 hd590300_1 conda-forge libxml2 2.13.7 h8d12d68_0 conda-forge libxslt 1.1.39 h76b75d6_0 conda-forge libzip 1.11.2 h6991a6a_0 conda-forge libzlib 1.3.1 hb9d3cd8_2 conda-forge llvm-openmp 20.1.1 h024ca30_1 conda-forge lxml 5.3.1 py312he28fd5a_0 conda-forge lz4-c 1.10.0 h5888daf_1 conda-forge markdown-it-py 3.0.0 pyhd8ed1ab_1 conda-forge markupsafe 3.0.2 py312h178313f_1 conda-forge matplotlib-base 3.10.1 py312hd3ec401_0 conda-forge matplotlib-inline 0.1.7 pyhd8ed1ab_1 conda-forge mctc-lib 0.3.2 h3b12eaf_1 conda-forge mda-xdrlib 0.2.0 pyhd8ed1ab_1 conda-forge mdtraj 1.10.3 py312h71c6f2c_0 conda-forge mdurl 0.1.2 pyhd8ed1ab_1 conda-forge mistune 3.1.3 pyh29332c3_0 conda-forge mkl 2024.2.2 ha957f24_16 conda-forge mpc 1.3.1 h24ddda3_1 conda-forge mpfr 4.2.1 h90cbb55_3 conda-forge mpmath 1.3.0 pyhd8ed1ab_1 conda-forge msgpack-python 1.1.0 py312h68727a3_0 conda-forge multicharge 0.3.0 hc15f34f_1 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge nbclient 0.10.2 pyhd8ed1ab_0 conda-forge nbconvert-core 7.16.6 pyh29332c3_0 conda-forge nbformat 5.10.4 pyhd8ed1ab_1 conda-forge ncurses 6.5 h2d0b736_3 conda-forge nest-asyncio 1.6.0 pyhd8ed1ab_1 conda-forge netcdf-fortran 4.6.1 nompi_h22f9119_108 conda-forge networkx 3.4.2 pyh267e887_2 conda-forge notebook 7.3.3 pyhd8ed1ab_0 conda-forge notebook-shim 0.2.4 pyhd8ed1ab_1 conda-forge numexpr 2.10.2 mkl_py312hacae085_0 conda-forge numpy 1.26.4 py312heda63a1_0 conda-forge ocl-icd 2.3.2 hb9d3cd8_2 conda-forge ocl-icd-system 1.0.0 1 conda-forge opencl-headers 2024.10.24 h5888daf_0 conda-forge openff-amber-ff-ports 0.0.4 pyhca7485f_0 conda-forge openff-bespokefit 0.4.2 pyhd8ed1ab_0 conda-forge openff-forcefields 2024.09.0 pyhff2d567_0 conda-forge openff-fragmenter-base 0.2.2 pyhd8ed1ab_0 conda-forge openff-interchange 0.3.29 pyhd8ed1ab_0 conda-forge openff-interchange-base 0.3.29 pyhd8ed1ab_0 conda-forge openff-models 0.1.2 pyhca7485f_0 conda-forge openff-qcsubmit 0.55.0 pyhd8ed1ab_1 conda-forge openff-toolkit 0.16.5 pyhd8ed1ab_0 conda-forge openff-toolkit-base 0.16.5 pyhd8ed1ab_0 conda-forge openff-units 0.2.2 pyhd8ed1ab_1 conda-forge openff-utilities 0.1.15 pyhd8ed1ab_0 conda-forge openjpeg 2.5.3 h5fbd93e_0 conda-forge openmm 8.2.0 py312haeaa2e4_2 conda-forge openssl 3.4.1 h7b32b05_0 conda-forge optree 0.14.1 py312h68727a3_1 conda-forge overrides 7.7.0 pyhd8ed1ab_1 conda-forge packaging 24.2 pyhd8ed1ab_2 conda-forge pandas 2.2.3 py312hf9745cd_1 conda-forge pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge panedr 0.8.0 pyhd8ed1ab_1 conda-forge parmed 4.3.0 py312ha9124a0_1 conda-forge parso 0.8.4 pyhd8ed1ab_1 conda-forge pcre2 10.44 hba22ea6_2 conda-forge perl 5.32.1 7_hd590300_perl5 conda-forge pexpect 4.9.0 pyhd8ed1ab_1 conda-forge pickleshare 0.7.5 pyhd8ed1ab_1004 conda-forge pillow 11.1.0 py312h80c1187_0 conda-forge pint 0.23 pyhd8ed1ab_1 conda-forge pip 25.0.1 pyh8b19718_0 conda-forge pixman 0.44.2 h29eaf8c_0 conda-forge pkgutil-resolve-name 1.3.10 pyhd8ed1ab_2 conda-forge platformdirs 4.3.7 pyh29332c3_0 conda-forge prometheus_client 0.21.1 pyhd8ed1ab_0 conda-forge prompt-toolkit 3.0.50 pyha770c72_0 conda-forge prompt_toolkit 3.0.50 hd8ed1ab_0 conda-forge psutil 7.0.0 py312h66e93f0_0 conda-forge pthread-stubs 0.4 hb9d3cd8_1002 conda-forge ptyprocess 0.7.0 pyhd8ed1ab_1 conda-forge pure_eval 0.2.3 pyhd8ed1ab_1 conda-forge py-cpuinfo 9.0.0 pyhd8ed1ab_1 conda-forge pybind11 2.13.6 pyh1ec8472_2 conda-forge pybind11-global 2.13.6 pyh415d2e4_2 conda-forge pycairo 1.27.0 py312h51b637d_0 conda-forge pycparser 2.22 pyh29332c3_1 conda-forge pydantic 1.10.17 py312h30e4e5e_1 conda-forge pyedr 0.8.0 pyhd8ed1ab_1 conda-forge pygments 2.19.1 pyhd8ed1ab_0 conda-forge pyjwt 2.10.1 pyhd8ed1ab_0 conda-forge pymbar 3.1.1 py312hcc4bcb2_3 conda-forge pyparsing 3.2.3 pyhd8ed1ab_1 conda-forge pysocks 1.7.1 pyha55dd90_7 conda-forge pytables 3.10.2 py312h2895ec7_2 conda-forge python 3.12.9 h9e4cc4f_1_cpython conda-forge python-constraint 1.4.0 pyhff2d567_1 conda-forge python-dateutil 2.9.0.post0 pyhff2d567_1 conda-forge python-dotenv 1.1.0 pyh29332c3_1 conda-forge python-fastjsonschema 2.21.1 pyhd8ed1ab_0 conda-forge python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge python-multipart 0.0.20 pyhff2d567_0 conda-forge python-tzdata 2025.2 pyhd8ed1ab_0 conda-forge python_abi 3.12 6_cp312 conda-forge pytorch 2.6.0 cpu_mkl_py312_he110f90_103 conda-forge pytz 2024.1 pyhd8ed1ab_0 conda-forge pyyaml 6.0.2 py312h178313f_2 conda-forge pyzmq 26.3.0 py312hbf22597_0 conda-forge qcelemental 0.28.0 pyhd8ed1ab_1 conda-forge qcengine 0.31.0 pyhd8ed1ab_0 conda-forge qcportal 0.54.1 pyhd8ed1ab_0 conda-forge qhull 2020.2 h434a139_5 conda-forge rdkit 2024.03.5 py312h7b4b7d0_3 conda-forge readline 8.2 h8c095d6_2 conda-forge redis-py 5.2.1 pyhd8ed1ab_1 conda-forge redis-server 7.4.0 h3400bea_0 conda-forge referencing 0.36.2 pyh29332c3_0 conda-forge regex 2024.11.6 py312h66e93f0_0 conda-forge reportlab 4.3.1 py312h66e93f0_0 conda-forge requests 2.32.3 pyhd8ed1ab_1 conda-forge rfc3339-validator 0.1.4 pyhd8ed1ab_1 conda-forge rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge rich 14.0.0 pyh29332c3_0 conda-forge rich-toolkit 0.11.3 pyh29332c3_0 conda-forge rlpycairo 0.2.0 pyhd8ed1ab_0 conda-forge rpds-py 0.24.0 py312h3b7be25_0 conda-forge s3transfer 0.11.4 pyhd8ed1ab_0 conda-forge scipy 1.15.2 py312ha707e6e_0 conda-forge send2trash 1.8.3 pyh0d859eb_1 conda-forge setuptools 75.8.2 pyhff2d567_0 conda-forge setuptools-scm 8.2.1 pyhd8ed1ab_0 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