fragmentation failed #290

xiki-tempula · 2023-10-13T10:09:46Z

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

The text was updated successfully, but these errors were encountered:

xiki-tempula · 2023-10-13T10:44:58Z

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

j-wags · 2023-10-13T17:13:17Z

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

j-wags · 2023-10-13T17:21:20Z

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 · 2023-10-14T13:27:50Z

@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 · 2023-10-16T19:29:24Z

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 · 2023-10-16T19:37:44Z

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

xiki-tempula · 2023-11-02T11:10:28Z

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.

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fragmentation failed #290

fragmentation failed #290

xiki-tempula commented Oct 13, 2023

packages in environment at /home/ubuntu/mambaforge/envs/bespokefit:

Name Version Build Channel

xiki-tempula commented Oct 13, 2023

j-wags commented Oct 13, 2023

j-wags commented Oct 13, 2023

xiki-tempula commented Oct 14, 2023

j-wags commented Oct 16, 2023

mattwthompson commented Oct 16, 2023

xiki-tempula commented Nov 2, 2023

fragmentation failed #290

fragmentation failed #290

Comments

xiki-tempula commented Oct 13, 2023

packages in environment at /home/ubuntu/mambaforge/envs/bespokefit:

Name Version Build Channel

xiki-tempula commented Oct 13, 2023

j-wags commented Oct 13, 2023

j-wags commented Oct 13, 2023

xiki-tempula commented Oct 14, 2023

j-wags commented Oct 16, 2023

mattwthompson commented Oct 16, 2023

xiki-tempula commented Nov 2, 2023