openff-bespokefit
openff-bespokefit copied to clipboard
openforcefield
fragmentation failed
Description
Hi, I have tried to install bespokefit with psi4 but got some dependency issue I guess. I create the env with
mamba create -n bespokefit -c psi4 -c conda-forge -c defaults -c openeye openff-bespokefit openeye-toolkits 'pint=0.21' python=3.10 'qcportal=0.15' psi4
Reproduction
I have first tried start the executer
openff-bespoke executor launch --directory "bespoke-executor" --n-fragmenter-workers 16 --n-optimizer-workers 12 --n-qc-compute-workers 32 --qc-compute-n-cores 8 --qc-compute-max-mem 40
Then I submit a cpmd and got this Output
────────────────────────────────────────────────────────────────────────────────────────────────── OpenFF Bespoke ──────────────────────────────────────────────────────────────────────────────────────────────────
[x] fragmentation failed
{"type": "ValueError", "message": "No registered toolkits can provide the capability \"assign_fractional_bond_orders\" for args \"(Molecule with name '' and SMILES
'[H]1([N]([H])[C](=[O])[C]([H])([H])[H])([H])([N]([H])[C](=[O])2([Cl])([H])([H])([H])2[Cl])1[H]',)\" and kwargs \"{'bond_order_model': 'am1-wiberg', 'use_conformers': [Quantity(value=array([[-2.02573424e+00,
2.09538481e-01, 1.79437257e+00],\n [ 5.36208593e+00, 6.53377680e-01, 1.16321291e+00],\n [-3.97166416e+00, -8.65996383e-01, 2.52411453e+00],\n [-2.59268990e+00, 4.95487335e-01,
-2.51041965e+00],\n [ 2.95720754e+00, 8.21550565e-01, 1.45568176e+00],\n [-2.06437081e+00, 3.75352420e-02, 5.17134732e-01],\n [ 5.30236327e+00, 1.24831111e-01, 3.30056745e-03],\n [
1.90566888e+00, 1.17176315e+00, 2.18897803e+00],\n [ 2.84690790e+00, 2.66919235e-01, 2.37100259e-01],\n [-6.01990653e+00, -7.20876549e-01, -9.15060273e-01],\n [-5.68406059e+00,
-8.86882309e-01, 4.05325138e-01],\n [-5.04890550e+00, -3.09622977e-01, -1.78875564e+00],\n [ 6.29293144e-01, 9.62723739e-01, 1.68989453e+00],\n [ 1.58518829e+00, 6.30233703e-02,
-2.49371962e-01],\n [-4.40211422e+00, -6.45673624e-01, 8.36698156e-01],\n [-3.74237087e+00, -6.63100355e-02, -1.33188527e+00],\n [-3.38181593e+00, -2.24258493e-01, -2.75315665e-02],\n [
4.17256639e-01, 4.03265355e-01, 4.59214358e-01],\n [ 4.00463468e+00, -9.84138395e-02, -5.26774770e-01],\n [-8.47718418e-01, 1.25025719e-01, -1.34437249e-01],\n [ 6.55014327e+00,
-2.35631677e-01, -7.47083151e-01],\n [ 2.00345489e+00, 1.61473148e+00, 3.16253576e+00],\n [-7.04093601e+00, -9.13762837e-01, -1.25730974e+00],\n [-6.43675946e+00, -1.21027481e+00,
1.10955296e+00],\n [-5.26588924e+00, -1.63033429e-01, -2.84957045e+00],\n [-2.31276939e-01, 1.26239557e+00, 2.28098895e+00],\n [ 1.49152001e+00, -3.83883486e-01, -1.23053574e+00],\n [
3.91188849e+00, -5.20251422e-01, -1.45392599e+00],\n [-8.12645667e-01, -4.29022359e-02, -1.17099858e+00],\n [ 6.49537610e+00, 1.38321984e-01, -1.78186185e+00],\n [ 6.70889743e+00,
-1.34219248e+00, -7.55597080e-01],\n [ 7.39697201e+00, 2.79476579e-01, -2.46412333e-01]]), unit=angstrom)]}\"\nAvailable toolkits are: [ToolkitWrapper around The RDKit version 2023.03.3, ToolkitWrapper
around Built-in Toolkit version None]\n", "traceback": "Traceback (most recent call last):\n File \"/home/ubuntu/mambaforge/envs/bespokefit/lib/python3.10/site-packages/celery/app/trace.py\", line 477, in
trace_task\n R = retval = fun(*args, **kwargs)\n File \"/home/ubuntu/mambaforge/envs/bespokefit/lib/python3.10/site-packages/celery/app/trace.py\", line 760, in __protected_call__\n return self.run(*args,
**kwargs)\n File \"/home/ubuntu/mambaforge/envs/bespokefit/lib/python3.10/site-packages/openff/bespokefit/executor/services/fragmenter/worker.py\", line 37, in fragment\n fragmenter.fragment(molecule,
target_bond_smarts=target_bond_smarts)\n File \"/home/ubuntu/mambaforge/envs/bespokefit/lib/python3.10/site-packages/openff/fragmenter/fragment.py\", line 916, in fragment\n result = self._fragment(molecule,
target_bond_smarts)\n File \"/home/ubuntu/mambaforge/envs/bespokefit/lib/python3.10/site-packages/openff/fragmenter/fragment.py\", line 1012, in _fragment\n molecule = assign_elf10_am1_bond_orders(\n File
\"/home/ubuntu/mambaforge/envs/bespokefit/lib/python3.10/site-packages/openff/fragmenter/chemi.py\", line 48, in assign_elf10_am1_bond_orders\n molecule.assign_fractional_bond_orders(\"am1-wiberg\",
use_conformers=)\n File \"/home/ubuntu/mambaforge/envs/bespokefit/lib/python3.10/site-packages/openff/toolkit/topology/molecule.py\", line 3473, in assign_fractional_bond_orders\n return
toolkit_registry.call(\n File \"/home/ubuntu/mambaforge/envs/bespokefit/lib/python3.10/site-packages/openff/toolkit/utils/toolkit_registry.py\", line 380, in call\n raise ValueError(msg)\nValueError: No
registered toolkits can provide the capability \"assign_fractional_bond_orders\" for args \"(Molecule with name '' and SMILES
'[H]1([N]([H])[C](=[O])[C]([H])([H])[H])([H])([N]([H])[C](=[O])2([Cl])([H])([H])([H])2[Cl])1[H]',)\" and kwargs \"{'bond_order_model': 'am1-wiberg', 'use_conformers': [Quantity(value=array([[-2.02573424e+00,
2.09538481e-01, 1.79437257e+00],\n [ 5.36208593e+00, 6.53377680e-01, 1.16321291e+00],\n [-3.97166416e+00, -8.65996383e-01, 2.52411453e+00],\n [-2.59268990e+00, 4.95487335e-01,
-2.51041965e+00],\n [ 2.95720754e+00, 8.21550565e-01, 1.45568176e+00],\n [-2.06437081e+00, 3.75352420e-02, 5.17134732e-01],\n [ 5.30236327e+00, 1.24831111e-01, 3.30056745e-03],\n [
1.90566888e+00, 1.17176315e+00, 2.18897803e+00],\n [ 2.84690790e+00, 2.66919235e-01, 2.37100259e-01],\n [-6.01990653e+00, -7.20876549e-01, -9.15060273e-01],\n [-5.68406059e+00,
-8.86882309e-01, 4.05325138e-01],\n [-5.04890550e+00, -3.09622977e-01, -1.78875564e+00],\n [ 6.29293144e-01, 9.62723739e-01, 1.68989453e+00],\n [ 1.58518829e+00, 6.30233703e-02,
-2.49371962e-01],\n [-4.40211422e+00, -6.45673624e-01, 8.36698156e-01],\n [-3.74237087e+00, -6.63100355e-02, -1.33188527e+00],\n [-3.38181593e+00, -2.24258493e-01, -2.75315665e-02],\n [
4.17256639e-01, 4.03265355e-01, 4.59214358e-01],\n [ 4.00463468e+00, -9.84138395e-02, -5.26774770e-01],\n [-8.47718418e-01, 1.25025719e-01, -1.34437249e-01],\n [ 6.55014327e+00,
-2.35631677e-01, -7.47083151e-01],\n [ 2.00345489e+00, 1.61473148e+00, 3.16253576e+00],\n [-7.04093601e+00, -9.13762837e-01, -1.25730974e+00],\n [-6.43675946e+00, -1.21027481e+00,
1.10955296e+00],\n [-5.26588924e+00, -1.63033429e-01, -2.84957045e+00],\n [-2.31276939e-01, 1.26239557e+00, 2.28098895e+00],\n [ 1.49152001e+00, -3.83883486e-01, -1.23053574e+00],\n [
3.91188849e+00, -5.20251422e-01, -1.45392599e+00],\n [-8.12645667e-01, -4.29022359e-02, -1.17099858e+00],\n [ 6.49537610e+00, 1.38321984e-01, -1.78186185e+00],\n [ 6.70889743e+00,
-1.34219248e+00, -7.55597080e-01],\n [ 7.39697201e+00, 2.79476579e-01, -2.46412333e-01]]), unit=angstrom)]}\"\nAvailable toolkits are: [ToolkitWrapper around The RDKit version 2023.03.3, ToolkitWrapper
around Built-in Toolkit version None]\n\n"}
Software versions
- Which operating system and version are you using? Linux
- How did you install BespokeFit? conda
- What is the output of running
conda list?
Output of conda list
packages in environment at /home/ubuntu/mambaforge/envs/bespokefit:
Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge ambit 0.6 py310h53dec33_2 psi4 amqp 5.1.1 pyhd8ed1ab_0 conda-forge anyio 3.7.1 pyhd8ed1ab_0 conda-forge argcomplete 3.1.2 pyhd8ed1ab_0 conda-forge asttokens 2.4.0 pyhd8ed1ab_0 conda-forge astunparse 1.6.3 pyhd8ed1ab_0 conda-forge async-timeout 4.0.3 pyhd8ed1ab_0 conda-forge attrs 23.1.0 pyh71513ae_1 conda-forge aws-c-auth 0.7.4 hc8144f4_1 conda-forge aws-c-cal 0.6.2 h09139f6_2 conda-forge aws-c-common 0.9.3 hd590300_0 conda-forge aws-c-compression 0.2.17 h184a658_3 conda-forge aws-c-event-stream 0.3.2 hd6ebb48_1 conda-forge aws-c-http 0.7.13 hc690213_1 conda-forge aws-c-io 0.13.32 h161b759_6 conda-forge aws-c-mqtt 0.9.6 h32970c0_2 conda-forge aws-c-s3 0.3.17 hb5e3142_3 conda-forge aws-c-sdkutils 0.1.12 h184a658_2 conda-forge aws-checksums 0.1.17 h184a658_2 conda-forge aws-crt-cpp 0.24.2 h94c364a_0 conda-forge aws-sdk-cpp 1.11.156 h314d761_4 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 pyhd8ed1ab_3 conda-forge backports.functools_lru_cache 1.6.5 pyhd8ed1ab_0 conda-forge backports.zoneinfo 0.2.1 py310hff52083_8 conda-forge basis_set_exchange 0.9.1 pyhd8ed1ab_0 conda-forge billiard 4.1.0 py310h2372a71_1 conda-forge blas 1.0 mkl conda-forge blosc 1.21.5 h0f2a231_0 conda-forge brotli 1.1.0 hd590300_1 conda-forge brotli-bin 1.1.0 hd590300_1 conda-forge brotli-python 1.1.0 py310hc6cd4ac_1 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.20.1 hd590300_0 conda-forge c-blosc2 2.10.5 hb4ffafa_0 conda-forge ca-certificates 2023.7.22 hbcca054_0 conda-forge cachetools 5.3.1 pyhd8ed1ab_0 conda-forge cairo 1.18.0 h3faef2a_0 conda-forge celery 5.3.4 pyhd8ed1ab_1 conda-forge certifi 2023.7.22 pyhd8ed1ab_0 conda-forge charset-normalizer 3.3.0 pyhd8ed1ab_0 conda-forge chemper 1.0.1 pyhd8ed1ab_0 conda-forge chemps2 1.8.11 hbe8a562_0 psi4 click 8.1.7 unix_pyh707e725_0 conda-forge click-didyoumean 0.3.0 pyhd8ed1ab_0 conda-forge click-option-group 0.5.6 pyhd8ed1ab_0 conda-forge click-plugins 1.1.1 py_0 conda-forge click-repl 0.3.0 pyhd8ed1ab_0 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge comm 0.1.4 pyhd8ed1ab_0 conda-forge contourpy 1.1.1 py310hd41b1e2_1 conda-forge cudatoolkit 11.8.0 h4ba93d1_12 conda-forge cycler 0.12.1 pyhd8ed1ab_0 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge dftd3 3.2.1 h84218bc_2 psi4 dkh 1.2 h173d85e_2 psi4 exceptiongroup 1.1.3 pyhd8ed1ab_0 conda-forge executing 1.2.0 pyhd8ed1ab_0 conda-forge expat 2.5.0 hcb278e6_1 conda-forge fastapi 0.86.0 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 hab24e00_0 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fonttools 4.43.1 py310h2372a71_0 conda-forge forcebalance 1.9.3 py310hc4a4660_2 conda-forge freetype 2.12.1 h267a509_2 conda-forge freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge future 0.18.3 pyhd8ed1ab_0 conda-forge gau2grid 2.0.7 hd18ef5c_0 psi4 gcp 2.0.2 he991be0_2 psi4 gdma 2.2.6 h0e1e685_6 psi4 geometric 1.0 pyhd8ed1ab_1 conda-forge gettext 0.21.1 h27087fc_0 conda-forge gflags 2.2.2 he1b5a44_1004 conda-forge glog 0.6.0 h6f12383_0 conda-forge greenlet 3.0.0 py310hc6cd4ac_1 conda-forge h11 0.14.0 pyhd8ed1ab_0 conda-forge h2 4.1.0 pyhd8ed1ab_0 conda-forge h5py 3.7.0 py310he06866b_0
hdf5 1.10.6 nompi_h3c11f04_101 conda-forge hpack 4.0.0 pyh9f0ad1d_0 conda-forge httpcore 0.18.0 pyhd8ed1ab_0 conda-forge httpx 0.25.0 pyhd8ed1ab_0 conda-forge hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge icu 73.2 h59595ed_0 conda-forge idna 3.4 pyhd8ed1ab_0 conda-forge importlib-metadata 6.8.0 pyha770c72_0 conda-forge importlib_resources 6.1.0 pyhd8ed1ab_0 conda-forge iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge intel-openmp 2021.4.0 h06a4308_3561
ipython 8.16.1 pyh0d859eb_0 conda-forge ipywidgets 8.1.1 pyhd8ed1ab_0 conda-forge jedi 0.19.1 pyhd8ed1ab_0 conda-forge jinja2 3.1.2 pyhd8ed1ab_1 conda-forge jsonschema 4.19.1 pyhd8ed1ab_0 conda-forge jsonschema-specifications 2023.7.1 pyhd8ed1ab_0 conda-forge jupyterlab_widgets 3.0.9 pyhd8ed1ab_0 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.5 py310hd41b1e2_1 conda-forge kombu 5.3.2 py310hff52083_1 conda-forge krb5 1.21.2 h659d440_0 conda-forge lcms2 2.15 hb7c19ff_3 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libabseil 20230802.1 cxx17_h59595ed_0 conda-forge libarrow 13.0.0 h75f0d2f_8_cpu conda-forge libblas 3.9.0 12_linux64_mkl conda-forge libboost 1.82.0 h6fcfa73_6 conda-forge libboost-python 1.82.0 py310hcb52e73_6 conda-forge libbrotlicommon 1.1.0 hd590300_1 conda-forge libbrotlidec 1.1.0 hd590300_1 conda-forge libbrotlienc 1.1.0 hd590300_1 conda-forge libcblas 3.9.0 12_linux64_mkl conda-forge libcrc32c 1.1.2 h9c3ff4c_0 conda-forge libcurl 8.4.0 hca28451_0 conda-forge libdeflate 1.19 hd590300_0 conda-forge libecpint 1.0.7 hfebba4c_0 psi4 libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libevent 2.1.12 hf998b51_1 conda-forge libexpat 2.5.0 hcb278e6_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 13.2.0 h807b86a_2 conda-forge libgfortran-ng 7.5.0 h14aa051_20 conda-forge libgfortran4 7.5.0 h14aa051_20 conda-forge libglib 2.78.0 hebfc3b9_0 conda-forge libgomp 13.2.0 h807b86a_2 conda-forge libgoogle-cloud 2.12.0 h19a6dae_3 conda-forge libgrpc 1.58.1 h30d5116_1 conda-forge libiconv 1.17 h166bdaf_0 conda-forge libint2 2.7.1 h2fe1556_15 psi4 libjpeg-turbo 3.0.0 hd590300_1 conda-forge liblapack 3.9.0 12_linux64_mkl conda-forge libnghttp2 1.52.0 h61bc06f_0 conda-forge libnsl 2.0.0 hd590300_1 conda-forge libnuma 2.0.16 h0b41bf4_1 conda-forge libpng 1.6.39 h753d276_0 conda-forge libprotobuf 4.24.3 hf27288f_1 conda-forge libsqlite 3.43.2 h2797004_0 conda-forge libssh2 1.11.0 h0841786_0 conda-forge libstdcxx-ng 13.2.0 h7e041cc_2 conda-forge libthrift 0.19.0 hb90f79a_1 conda-forge libtiff 4.6.0 ha9c0a0a_2 conda-forge libutf8proc 2.8.0 h166bdaf_0 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libwebp-base 1.3.2 hd590300_0 conda-forge libxc 5.2.3 hfebba4c_0 psi4 libxcb 1.15 h0b41bf4_0 conda-forge libxml2 2.11.5 h232c23b_1 conda-forge libxslt 1.1.37 h0054252_1 conda-forge libzlib 1.2.13 hd590300_5 conda-forge lxml 4.9.3 py310h9b7343a_1 conda-forge lz4-c 1.9.4 hcb278e6_0 conda-forge lzo 2.10 h516909a_1000 conda-forge markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge markupsafe 2.1.3 py310h2372a71_1 conda-forge matplotlib-base 3.8.0 py310h62c0568_2 conda-forge matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge mdtraj 1.9.9 py310h8e08b51_0 conda-forge mdurl 0.1.0 pyhd8ed1ab_0 conda-forge mkl 2021.4.0 h06a4308_640
mkl-service 2.4.0 py310ha2c4b55_0 conda-forge msgpack-python 1.0.6 py310hd41b1e2_0 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge ncurses 6.4 hcb278e6_0 conda-forge networkx 3.1 pyhd8ed1ab_0 conda-forge nglview 3.0.8 pyh1da8cd4_0 conda-forge numexpr 2.7.3 py310hb5077e9_1 conda-forge numpy 1.22.4 py310h4ef5377_0 conda-forge ocl-icd 2.3.1 h7f98852_0 conda-forge ocl-icd-system 1.0.0 1 conda-forge openeye-toolkits 2023.1.1 py310_0 openeye openff-bespokefit 0.1.3 pyhd8ed1ab_3 conda-forge openff-forcefields 2023.08.0 pyh1a96a4e_0 conda-forge openff-fragmenter-base 0.1.2 pyhd8ed1ab_1 conda-forge openff-qcsubmit 0.3.2 pyhd8ed1ab_0 conda-forge openff-toolkit-base 0.10.7 pyhd8ed1ab_0 conda-forge openff-utilities 0.1.10 pyhd8ed1ab_0 conda-forge openjpeg 2.5.0 h488ebb8_3 conda-forge openmm 8.0.0 py310h4812340_3 conda-forge openssl 3.1.3 hd590300_0 conda-forge optking 0.2.1 pyhbc12335_1 psi4 orc 1.9.0 h208142c_3 conda-forge packaging 23.2 pyhd8ed1ab_0 conda-forge pandas 1.4.4 py310h769672d_0 conda-forge parso 0.8.3 pyhd8ed1ab_0 conda-forge pcmsolver 1.2.1.1 py310h92d4acf_3 psi4 pcre2 10.40 hc3806b6_0 conda-forge pexpect 4.8.0 pyh1a96a4e_2 conda-forge pickleshare 0.7.5 py_1003 conda-forge pillow 10.0.1 py310h01dd4db_2 conda-forge pint 0.21 pyhd8ed1ab_0 conda-forge pip 23.2.1 pyhd8ed1ab_0 conda-forge pixman 0.42.2 h59595ed_0 conda-forge pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge plotly 5.17.0 pyhd8ed1ab_0 conda-forge pluggy 1.3.0 pyhd8ed1ab_0 conda-forge prompt-toolkit 3.0.39 pyha770c72_0 conda-forge prompt_toolkit 3.0.39 hd8ed1ab_0 conda-forge psi4 1.7+6ce35a5 py310h769327c_1 psi4 psutil 5.9.5 py310h2372a71_1 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge py-cpuinfo 9.0.0 pyhd8ed1ab_0 conda-forge pyarrow 13.0.0 py310hf9e7431_8_cpu conda-forge pycairo 1.25.0 py310hda9f760_1 conda-forge pydantic 1.10.13 py310h2372a71_0 conda-forge pygments 2.16.1 pyhd8ed1ab_0 conda-forge pymbar 3.1.1 py310hde88566_2 conda-forge pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge pytables 3.8.0 py310h43249b6_2
pytest 7.4.2 pyhd8ed1ab_0 conda-forge python 3.10.12 hd12c33a_0_cpython conda-forge python-constraint 1.4.0 py_0 conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge python_abi 3.10 4_cp310 conda-forge pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge pyyaml 6.0.1 py310h2372a71_1 conda-forge qcelemental 0.25.1 pyhd8ed1ab_1 psi4 qcengine 0.26.0 pyhd8ed1ab_0 psi4 qcportal 0.15.8 pyhd8ed1ab_1 conda-forge rdkit 2023.03.3 py310hb79e901_1 conda-forge rdma-core 28.9 h59595ed_1 conda-forge re2 2023.03.02 h8c504da_0 conda-forge readline 8.2 h8228510_1 conda-forge redis-py 5.0.1 pyhd8ed1ab_0 conda-forge redis-server 7.2.1 h06160fa_0 conda-forge referencing 0.30.2 pyhd8ed1ab_0 conda-forge regex 2023.10.3 py310h2372a71_0 conda-forge reportlab 4.0.6 py310h2372a71_0 conda-forge requests 2.31.0 pyhd8ed1ab_0 conda-forge rich 13.6.0 pyhd8ed1ab_0 conda-forge rlpycairo 0.2.0 pyhd8ed1ab_0 conda-forge rpds-py 0.10.6 py310hcb5633a_0 conda-forge s2n 1.3.54 h06160fa_0 conda-forge scipy 1.7.3 py310hfa59a62_0
setuptools 68.2.2 pyhd8ed1ab_0 conda-forge simint 0.7 h642920c_1 psi4 six 1.16.0 pyh6c4a22f_0 conda-forge smirnoff99frosst 1.1.0 pyh44b312d_0 conda-forge snappy 1.1.10 h9fff704_0 conda-forge sniffio 1.3.0 pyhd8ed1ab_0 conda-forge sqlalchemy 2.0.21 py310h2372a71_1 conda-forge stack_data 0.6.2 pyhd8ed1ab_0 conda-forge starlette 0.20.4 pyhd8ed1ab_1 conda-forge tenacity 8.2.3 pyhd8ed1ab_0 conda-forge tk 8.6.13 h2797004_0 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge torsiondrive 1.1.0 pyhd8ed1ab_0 conda-forge tqdm 4.66.1 pyhd8ed1ab_0 conda-forge traitlets 5.11.2 pyhd8ed1ab_0 conda-forge typing-extensions 4.8.0 hd8ed1ab_0 conda-forge typing_extensions 4.8.0 pyha770c72_0 conda-forge tzdata 2023c h71feb2d_0 conda-forge ucx 1.15.0 h64cca9d_0 conda-forge unicodedata2 15.1.0 py310h2372a71_0 conda-forge unidecode 1.3.7 pyhd8ed1ab_0 conda-forge urllib3 2.0.6 pyhd8ed1ab_0 conda-forge uvicorn 0.23.2 py310hff52083_1 conda-forge vine 5.0.0 pyhd8ed1ab_1 conda-forge wcwidth 0.2.8 pyhd8ed1ab_0 conda-forge wheel 0.41.2 pyhd8ed1ab_0 conda-forge widgetsnbextension 4.0.9 pyhd8ed1ab_0 conda-forge xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.1.1 hd590300_0 conda-forge xorg-libsm 1.2.4 h7391055_0 conda-forge xorg-libx11 1.8.7 h8ee46fc_0 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxrender 0.9.11 hd590300_0 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 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 zipp 3.17.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 hd590300_5 conda-forge zlib-ng 2.0.7 h0b41bf4_0 conda-forge zstd 1.5.5 hfc55251_0 conda-forge
Weird that this problem only happens on the R7a instance but not m6i instance.
Could you double check that OpenEye is installed and that the license is present and unexpired?
Oh, you helpfully included the conda list output showing that OE is installed - thanks for that. Could you also double check your license is valid?
@j-wags Yes. The license is valid. I think this seems to be a weird issue with regard only to the AWS EC2 R7a instance. If I connect the EBS (which is the hard disk) to a R6i instance, it is totally fine. Connecting the EBS to another instance means that everything in the hard drive is reconnected.
Hmm, OK. I don't have much experience with running things on AWS. The part of your report that stands out to me is that the OpenFF Toolkit didn't even try running with OpenEye:
nAvailable toolkits are: [ToolkitWrapper around The RDKit version 2023.03.3, ToolkitWrapper around Built-in Toolkit version None]\n\n"}
The two causes that I know for this are either installation or license issues... There may be a more subtle/complex failure mode on AWS that I just haven't seen before.
How can we reproduce this issue? Presumably you ran openff-bespoke executor submit at some point?
Yes. I
do
openff-bespoke executor launch --directory "bespoke-executor" --n-fragmenter-workers 16 --n-optimizer-workers 12 --n-qc-compute-workers 32 --qc-compute-n-cores 8 --qc-compute-max-mem 4
first Then do
openff-bespoke executor submit --smiles "CC(=O)NC1=CC=C(C=C1)O" \
--workflow "default" \
--default-qc-spec xtb gfn2xtb none
I think you could reproduce this problem with any AWS R7a instance. Note that Both C7i and M6i instance don't have this problem and seems to only happen to R7a.