fragmentation failed - Githubissues

xiki-tempula commented 11 months ago

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

xiki-tempula commented 11 months ago

Weird that this problem only happens on the R7a instance but not m6i instance.

j-wags commented 11 months ago

Could you double check that OpenEye is installed and that the license is present and unexpired?

j-wags commented 11 months ago

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?

xiki-tempula commented 11 months ago

@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.

j-wags commented 11 months ago

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.

mattwthompson commented 11 months ago

How can we reproduce this issue? Presumably you ran openff-bespoke executor submit at some point?

xiki-tempula commented 10 months ago

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.

openforcefield / openff-bespokefit

fragmentation failed #290