Optimization error encountered when following tutorial

[orionarcher]

Description

Hello! I am again trying to follow the instructions in the tutorial (now for the CLI) but I ran into an optimization error when exactly following the tutorial. I am not sure where to begin in debugging this.

Reproduction

openff-bespoke executor run --smiles             "CC(=O)NC1=CC=C(C=C1)O" \
                            --workflow           "default"               \
                            --output             "acetaminophen.json"    \
                            --output-force-field "acetaminophen.offxml"  \
                            --n-qc-compute-workers 2                     \
                            --qc-compute-n-cores   1                     \
                            --default-qc-spec xtb gfn2xtb none

Output

Error 1:

───────────────────────────────────────────────────────────────────────────────────────────────────────────────── OpenFF Bespoke ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────

[✓] bespoke executor launched

1. preparing the bespoke workflow                                                                                                                                                                                                                 

[✓] 1 molecules found
[✓] fitting schemas generated

2. submitting the workflow                                                                                                                                                                                                                        

[✓] the following workflows were submitted
┏━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━┓
┃ ID ┃ SMILES             ┃ NAME ┃ FILE ┃
┡━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━╇━━━━━━┩
│ 1  │ CC(=O)Nc1ccc(O)cc1 │      │      │
└────┴────────────────────┴──────┴──────┘

3. running the fitting pipeline                                                                                                                                                                                                                   

[✓] fragmentation successful
[✓] qc-generation successful
⠋ optimizing the parametersobjc[74316]: +[__NSCFConstantString initialize] may have been in progress in another thread when fork() was called.
objc[74316]: +[__NSCFConstantString initialize] may have been in progress in another thread when fork() was called. We cannot safely call it or ignore it in the fork() child process. Crashing instead. Set a breakpoint on objc_initializeAfterForkError to debug.
[x] optimization failed

 {"type": "WorkerLostError", "message": "Worker exited prematurely: signal 6 (SIGABRT) Job: 0.", "traceback": null}                                                                                                                               

outputs have been saved to acetaminophen.json                                                                                                                                                                                                     

worker: Warm shutdown (MainProcess)

worker: Warm shutdown (MainProcess)

worker: Warm shutdown (MainProcess)

Software versions

• Which operating system and version are you using? macOS Monterey 12.7.4
• How did you install BespokeFit? Via mamba.
• Are you using Apple Silicon? If so, are you running BespokeFit in Rosetta (osx-64) or natively (osx-arm64)? No.
• What is the output of running conda list?

I admit, my conda environment is quite messy.

Output of conda list

conda list
# packages in environment at /Users/orioncohen/miniconda3/envs/atomate_emmet:
#
# Name                    Version                   Build  Channel
aiohttp                   3.9.3                    pypi_0    pypi
aioitertools              0.11.0                   pypi_0    pypi
aiosignal                 1.3.1                    pypi_0    pypi
ambertools                23.3            py311hb11241e_6    conda-forge
amberutils                21.0                     pypi_0    pypi
amqp                      5.2.0              pyhd8ed1ab_1    conda-forge
annotated-types           0.6.0              pyhd8ed1ab_0    conda-forge
anyio                     4.3.0              pyhd8ed1ab_0    conda-forge
appnope                   0.1.4              pyhd8ed1ab_0    conda-forge
apsw                      3.45.2.0        py311hd50245e_1    conda-forge
archspec                  0.2.3              pyhd8ed1ab_0    conda-forge
argcomplete               3.3.0              pyhd8ed1ab_0    conda-forge
argon2-cffi               23.1.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py311h2725bcf_4    conda-forge
arpack                    3.8.0           nompi_hb44a6d1_101    conda-forge
arrow                     1.3.0              pyhd8ed1ab_0    conda-forge
ase                       3.22.1                   pypi_0    pypi
asttokens                 2.4.1              pyhd8ed1ab_0    conda-forge
astunparse                1.6.3              pyhd8ed1ab_0    conda-forge
async-lru                 2.0.4              pyhd8ed1ab_0    conda-forge
async-timeout             4.0.3              pyhd8ed1ab_0    conda-forge
atomate2                  0.0.12.post488+geb225715          pypi_0    pypi
attrs                     23.2.0             pyh71513ae_0    conda-forge
babel                     2.14.0             pyhd8ed1ab_0    conda-forge
backports.zoneinfo        0.2.1           py311h6eed73b_8    conda-forge
basis_set_exchange        0.10               pyhd8ed1ab_1    conda-forge
bcrypt                    4.1.2           py311h5e0f0e4_0    conda-forge
beautifulsoup4            4.12.3             pyha770c72_0    conda-forge
billiard                  4.2.0           py311he705e18_0    conda-forge
biopython                 1.83            py311he705e18_0    conda-forge
black                     24.3.0                   pypi_0    pypi
bleach                    6.1.0              pyhd8ed1ab_0    conda-forge
blinker                   1.7.0              pyhd8ed1ab_0    conda-forge
blosc                     1.21.5               heccf04b_0    conda-forge
boltons                   24.0.0             pyhd8ed1ab_0    conda-forge
boto3                     1.34.73                  pypi_0    pypi
botocore                  1.34.73                  pypi_0    pypi
brotli                    1.1.0                h0dc2134_1    conda-forge
brotli-bin                1.1.0                h0dc2134_1    conda-forge
brotli-python             1.1.0           py311hdf8f085_1    conda-forge
bson                      0.5.9                      py_0    conda-forge
bzip2                     1.0.8                h10d778d_5    conda-forge
c-ares                    1.28.0               h10d778d_0    conda-forge
c-blosc2                  2.12.0               h0ae8482_0    conda-forge
ca-certificates           2024.2.2             h8857fd0_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cachetools                5.3.3              pyhd8ed1ab_0    conda-forge
cairo                     1.18.0               h99e66fa_0    conda-forge
celery                    5.3.6              pyhd8ed1ab_0    conda-forge
certifi                   2024.2.2           pyhd8ed1ab_0    conda-forge
cffi                      1.16.0          py311hc0b63fd_0    conda-forge
cfgv                      3.4.0                    pypi_0    pypi
cftime                    1.6.3           py311hc9a392d_0    conda-forge
chardet                   5.2.0           py311h6eed73b_1    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
chemper                   1.0.1              pyhd8ed1ab_0    conda-forge
chgnet                    0.3.5                    pypi_0    pypi
click                     8.1.7           unix_pyh707e725_0    conda-forge
click-didyoumean          0.3.1              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                      0.2.2              pyhd8ed1ab_0    conda-forge
conda                     24.5.0          py311h6eed73b_0    conda-forge
conda-libmamba-solver     24.1.0             pyhd8ed1ab_0    conda-forge
conda-package-handling    2.2.0              pyh38be061_0    conda-forge
conda-package-streaming   0.9.0              pyhd8ed1ab_0    conda-forge
contourpy                 1.2.0           py311h7bea37d_0    conda-forge
cryptography              42.0.5          py311hda9c3b6_0    conda-forge
custodian                 2024.3.12                pypi_0    pypi
cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
cython                    3.0.9                    pypi_0    pypi
debugpy                   1.8.1           py311hdd0406b_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
deprecated                1.2.14             pyh1a96a4e_0    conda-forge
dftd3-python              1.0.0           py311hcded3c8_1    conda-forge
dgl                       2.1.0                    pypi_0    pypi
distlib                   0.3.8                    pypi_0    pypi
distro                    1.9.0              pyhd8ed1ab_0    conda-forge
dkh                       1.2                  hb57fcd4_0    conda-forge
dnspython                 2.6.1              pyhd8ed1ab_1    conda-forge
edgembar                  0.2                      pypi_0    pypi
ele                       0.2.0              pyhd8ed1ab_0    conda-forge
email-validator           2.1.1              pyhd8ed1ab_0    conda-forge
email_validator           2.1.1                hd8ed1ab_0    conda-forge
emmet-builders            0.37.1.dev870+gbb17c5e2           dev_0    
emmet-core                0.82.2.dev71+gd834d38f.d20240507           dev_0    
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
et-xmlfile                1.1.0                    pypi_0    pypi
exceptiongroup            1.2.0              pyhd8ed1ab_2    conda-forge
executing                 2.0.1              pyhd8ed1ab_0    conda-forge
expat                     2.6.2                h73e2aa4_0    conda-forge
fabric                    3.2.2              pyhd8ed1ab_0    conda-forge
fastapi                   0.110.0                  pypi_0    pypi
fastapi-cli               0.0.4              pyhd8ed1ab_0    conda-forge
fasteners                 0.19                     pypi_0    pypi
fftw                      3.3.10          nompi_h4fa670e_108    conda-forge
filelock                  3.13.3                   pypi_0    pypi
fireworks                 2.0.3              pyhd8ed1ab_0    conda-forge
flask                     3.0.2                    pypi_0    pypi
flask-paginate            2024.3.28          pyhd8ed1ab_0    conda-forge
fmt                       10.2.1               h7728843_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_1    conda-forge
fontconfig                2.14.2               h5bb23bf_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.50.0          py311he705e18_0    conda-forge
forcebalance              1.9.6           py311h7c2fe40_2    conda-forge
forcefield-utilities      0.2.2              pyhd8ed1ab_0    conda-forge
foyer                     0.12.1             pyhd8ed1ab_0    conda-forge
fqdn                      1.5.1              pyhd8ed1ab_0    conda-forge
freetype                  2.12.1               h60636b9_2    conda-forge
freetype-py               2.3.0              pyhd8ed1ab_0    conda-forge
frozendict                2.4.4           py311h72ae277_0    conda-forge
frozenlist                1.4.1                    pypi_0    pypi
fsspec                    2024.3.1                 pypi_0    pypi
future                    1.0.0              pyhd8ed1ab_0    conda-forge
gau2grid                  2.0.7                hb7f2c08_2    conda-forge
geometric                 1.0                pyhd8ed1ab_1    conda-forge
gettext                   0.21.1               h8a4c099_0    conda-forge
gf2x                      1.3.0                hb2a7efb_2    conda-forge
glpk                      5.0                  h3cb5acd_0    conda-forge
gmp                       6.3.0                h73e2aa4_1    conda-forge
gmpy2                     2.1.5           py311hab17429_1    conda-forge
gmso                      0.11.2             pyhd8ed1ab_0    conda-forge
greenlet                  3.0.3           py311hdd0406b_0    conda-forge
griddataformats           1.0.2              pyhd8ed1ab_0    conda-forge
gsd                       3.2.1           py311hc9a392d_0    conda-forge
gtest                     1.14.0               h1c7c39f_1    conda-forge
gunicorn                  21.2.0          py311h6eed73b_1    conda-forge
h11                       0.14.0             pyhd8ed1ab_0    conda-forge
h2                        4.1.0              pyhd8ed1ab_0    conda-forge
h5py                      3.10.0          nompi_py311hf7b785c_101    conda-forge
hdf4                      4.2.15               h8138101_7    conda-forge
hdf5                      1.14.3          nompi_h691f4bf_100    conda-forge
hpack                     4.0.0              pyh9f0ad1d_0    conda-forge
httpcore                  1.0.5              pyhd8ed1ab_0    conda-forge
httpx                     0.27.0             pyhd8ed1ab_0    conda-forge
hyperframe                6.0.1              pyhd8ed1ab_0    conda-forge
icu                       73.2                 hf5e326d_0    conda-forge
identify                  2.5.35                   pypi_0    pypi
idna                      3.6                pyhd8ed1ab_0    conda-forge
importlib-metadata        7.1.0              pyha770c72_0    conda-forge
importlib_metadata        7.1.0                hd8ed1ab_0    conda-forge
importlib_resources       6.4.0              pyhd8ed1ab_0    conda-forge
inflect                   7.0.0                    pypi_0    pypi
iniconfig                 2.0.0              pyhd8ed1ab_0    conda-forge
invoke                    2.2.0              pyhd8ed1ab_0    conda-forge
ipykernel                 6.29.3             pyh3cd1d5f_0    conda-forge
ipython                   8.22.2             pyh707e725_0    conda-forge
ipywidgets                8.1.2              pyhd8ed1ab_0    conda-forge
isoduration               20.11.0            pyhd8ed1ab_0    conda-forge
itsdangerous              2.1.2              pyhd8ed1ab_0    conda-forge
jedi                      0.19.1             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.3              pyhd8ed1ab_0    conda-forge
jmespath                  1.0.1              pyhd8ed1ab_0    conda-forge
jobflow                   0.1.17                   pypi_0    pypi
joblib                    1.3.2              pyhd8ed1ab_0    conda-forge
json5                     0.9.24             pyhd8ed1ab_0    conda-forge
jsonpatch                 1.33               pyhd8ed1ab_0    conda-forge
jsonpointer               2.4             py311h6eed73b_3    conda-forge
jsonschema                4.21.1             pyhd8ed1ab_0    conda-forge
jsonschema-specifications 2023.12.1          pyhd8ed1ab_0    conda-forge
jsonschema-with-format-nongpl 4.21.1             pyhd8ed1ab_0    conda-forge
jupyter-lsp               2.2.4              pyhd8ed1ab_0    conda-forge
jupyter_client            8.6.1              pyhd8ed1ab_0    conda-forge
jupyter_core              5.7.2           py311h6eed73b_0    conda-forge
jupyter_events            0.10.0             pyhd8ed1ab_0    conda-forge
jupyter_server            2.13.0             pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.5.3              pyhd8ed1ab_0    conda-forge
jupyterlab                4.1.5              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.3.0              pyhd8ed1ab_1    conda-forge
jupyterlab_server         2.25.4             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.10             pyhd8ed1ab_0    conda-forge
khronos-opencl-icd-loader 2023.04.17           hb7f2c08_0    conda-forge
kiwisolver                1.4.5           py311h5fe6e05_1    conda-forge
kombu                     5.3.7           py311h6eed73b_0    conda-forge
krb5                      1.21.2               hb884880_0    conda-forge
lark-parser               0.12.0             pyhd8ed1ab_0    conda-forge
latexcodec                3.0.0                    pypi_0    pypi
lcms2                     2.16                 ha2f27b4_0    conda-forge
lerc                      4.0.0                hb486fe8_0    conda-forge
libabseil                 20240116.2      cxx17_hc1bcbd7_0    conda-forge
libaec                    1.1.3                h73e2aa4_0    conda-forge
libarchive                3.7.2                hd35d340_1    conda-forge
libblas                   3.9.0              20_osx64_mkl    conda-forge
libboost                  1.82.0               h99d8d82_6    conda-forge
libboost-python           1.82.0          py311h3b8bc05_6    conda-forge
libbrotlicommon           1.1.0                h0dc2134_1    conda-forge
libbrotlidec              1.1.0                h0dc2134_1    conda-forge
libbrotlienc              1.1.0                h0dc2134_1    conda-forge
libcblas                  3.9.0              20_osx64_mkl    conda-forge
libcurl                   8.7.1                h726d00d_0    conda-forge
libcxx                    16.0.6               hd57cbcb_0    conda-forge
libdeflate                1.20                 h49d49c5_0    conda-forge
libecpint                 1.0.7               h8253960_10    conda-forge
libedit                   3.1.20191231         h0678c8f_2    conda-forge
libev                     4.33                 h10d778d_2    conda-forge
libexpat                  2.6.2                h73e2aa4_0    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libflint                  2.9.0           hfd2f71f_ntl_100    conda-forge
libgfortran               5.0.0           13_2_0_h97931a8_3    conda-forge
libgfortran5              13.2.0               h2873a65_3    conda-forge
libglib                   2.80.0               h81c1438_1    conda-forge
libhwloc                  2.10.0          default_h1321489_1000    conda-forge
libiconv                  1.17                 hd75f5a5_2    conda-forge
libint                    2.9.0                hf344f97_0    conda-forge
libjpeg-turbo             3.0.0                h0dc2134_1    conda-forge
liblapack                 3.9.0              20_osx64_mkl    conda-forge
libmamba                  1.5.8                ha449628_0    conda-forge
libmambapy                1.5.8           py311h6c5c7ae_0    conda-forge
libnetcdf                 4.9.2           nompi_h7760872_113    conda-forge
libnghttp2                1.58.0               h64cf6d3_1    conda-forge
libopenblas               0.3.26          openmp_hfef2a42_0    conda-forge
libpcm                    1.2.3                hf5d0054_8    conda-forge
libpng                    1.6.43               h92b6c6a_0    conda-forge
libprotobuf               4.25.3               h4e4d658_0    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
libsolv                   0.7.29               h4f92f52_0    conda-forge
libsqlite                 3.45.2               h92b6c6a_0    conda-forge
libssh2                   1.11.0               hd019ec5_0    conda-forge
libtiff                   4.6.0                h129831d_3    conda-forge
libwebp-base              1.3.2                h0dc2134_0    conda-forge
libxc-c                   6.2.2            cpu_hebaf863_4    conda-forge
libxcb                    1.15                 hb7f2c08_0    conda-forge
libxml2                   2.12.6               hc0ae0f7_1    conda-forge
libxslt                   1.1.39               h03b04e6_0    conda-forge
libzip                    1.10.1               hc158999_3    conda-forge
libzlib                   1.2.13               h8a1eda9_5    conda-forge
lightning-utilities       0.11.2                   pypi_0    pypi
llvm-openmp               18.1.2               hb6ac08f_0    conda-forge
lxml                      5.2.2           py311hf8c4076_0    conda-forge
lz4-c                     1.9.4                hf0c8a7f_0    conda-forge
lzo                       2.10              h10d778d_1001    conda-forge
maggma                    0.64.0                   pypi_0    pypi
mamba                     1.5.8           py311h8082e30_0    conda-forge
markdown-it-py            3.0.0              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.5           py311he705e18_0    conda-forge
matcalc                   0.0.4                    pypi_0    pypi
matgl                     1.0.0                    pypi_0    pypi
matminer                  0.9.2                    pypi_0    pypi
matplotlib-base           3.8.3           py311h6ff1f5f_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mctc-lib                  0.3.1                h5f0aba5_0    conda-forge
mda-xdrlib                0.2.0              pyhd8ed1ab_0    conda-forge
mdahole2                  0.4.0                    pypi_0    pypi
mdanalysis                2.8.0.dev0               pypi_0    pypi
mdareporter               0.1+3.gd665b3d           pypi_0    pypi
mdtraj                    1.9.9           py311h8f92aaa_0    conda-forge
mdurl                     0.1.2              pyhd8ed1ab_0    conda-forge
menuinst                  2.1.0           py311h6eed73b_0    conda-forge
mistune                   3.0.2              pyhd8ed1ab_0    conda-forge
mkl                       2023.2.0         h54c2260_50500    conda-forge
mmpbsa-py                 16.0                     pypi_0    pypi
mmtf-python               1.1.3              pyhd8ed1ab_0    conda-forge
mongogrant                0.3.3                    pypi_0    pypi
mongomock                 4.1.2                    pypi_0    pypi
monty                     2024.2.26          pyhd8ed1ab_0    conda-forge
mpc                       1.3.1                h81bd1dd_0    conda-forge
mpfr                      4.2.1                h4f6b447_1    conda-forge
mpi                       1.0                     openmpi    conda-forge
mpi4py                    3.1.6           py311hf2bceb4_0    conda-forge
mpmath                    1.3.0              pyhd8ed1ab_0    conda-forge
mrcfile                   1.5.0              pyhd8ed1ab_0    conda-forge
msgpack                   1.0.8                    pypi_0    pypi
msgpack-python            1.0.7           py311h7bea37d_0    conda-forge
multidict                 6.0.5                    pypi_0    pypi
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
mypy                      1.9.0                    pypi_0    pypi
mypy-extensions           1.0.0                    pypi_0    pypi
nbclient                  0.10.0             pyhd8ed1ab_0    conda-forge
nbconvert-core            7.16.3             pyhd8ed1ab_0    conda-forge
nbformat                  5.10.3             pyhd8ed1ab_0    conda-forge
ncurses                   6.4.20240210         h73e2aa4_0    conda-forge
nest-asyncio              1.6.0              pyhd8ed1ab_0    conda-forge
netcdf-fortran            4.6.1           nompi_h383bc5a_103    conda-forge
netcdf4                   1.6.5           nompi_py311hd2be13f_100    conda-forge
networkx                  3.2.1              pyhd8ed1ab_0    conda-forge
nglview                   3.1.2              pyh15ce09e_0    conda-forge
nodeenv                   1.8.0                    pypi_0    pypi
notebook                  7.1.2              pyhd8ed1ab_0    conda-forge
notebook-shim             0.2.4              pyhd8ed1ab_0    conda-forge
ntl                       11.4.3               h0ab3c2f_1    conda-forge
numexpr                   2.9.0           py311h8f6166a_0    conda-forge
numpy                     1.26.4          py311hc43a94b_0    conda-forge
nvidia-ml-py3             7.352.0                  pypi_0    pypi
ocl_icd_wrapper_apple     1.0.0                hbcb3906_0    conda-forge
openbabel                 3.1.1           py311he4d38a6_9    conda-forge
openff-amber-ff-ports     0.0.4              pyhca7485f_0    conda-forge
openff-bespokefit         0.3.0              pyhd8ed1ab_0    conda-forge
openff-forcefields        2024.03.0          pyhca7485f_0    conda-forge
openff-fragmenter-base    0.2.1              pyhd8ed1ab_0    conda-forge
openff-interchange        0.3.25             pyhd8ed1ab_0    conda-forge
openff-interchange-base   0.3.25             pyhd8ed1ab_0    conda-forge
openff-models             0.1.2              pyhca7485f_0    conda-forge
openff-qcsubmit           0.51.0             pyhd8ed1ab_0    conda-forge
openff-toolkit            0.15.2             pyhd8ed1ab_0    conda-forge
openff-toolkit-base       0.15.2             pyhd8ed1ab_0    conda-forge
openff-units              0.2.2              pyhca7485f_0    conda-forge
openff-utilities          0.1.12             pyhd8ed1ab_0    conda-forge
openjpeg                  2.5.2                h7310d3a_0    conda-forge
openmm                    8.1.1           py311h2827df7_1_khronos    conda-forge
openmm-mdanalysis-reporter 0.1                      pypi_0    pypi
openmpi                   4.1.6              h7406208_101    conda-forge
openpyxl                  3.1.2                    pypi_0    pypi
openssl                   3.3.0                h87427d6_3    conda-forge
optking                   0.2.1              pyhd8ed1ab_0    conda-forge
orjson                    3.10.0                   pypi_0    pypi
overrides                 7.7.0              pyhd8ed1ab_0    conda-forge
packaging                 24.0               pyhd8ed1ab_0    conda-forge
packmol                   20.010               h508aa58_0    conda-forge
packmol-memgen            2023.2.24                pypi_0    pypi
palettable                3.3.3                    pypi_0    pypi
pandas                    2.2.1           py311h8f6166a_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
panedr                    0.8.0              pyhd8ed1ab_0    conda-forge
paramiko                  3.4.0              pyhd8ed1ab_0    conda-forge
parmed                    4.2.2           py311hd39e593_1    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pathlib2                  2.3.7.post1     py311h6eed73b_3    conda-forge
pathsimanalysis           1.1.0                    pypi_0    pypi
pathspec                  0.12.1                   pypi_0    pypi
patsy                     0.5.6              pyhd8ed1ab_0    conda-forge
pcmsolver                 1.2.3                      py_9    conda-forge
pcre2                     10.43                h0ad2156_0    conda-forge
pdb4amber                 22.0                     pypi_0    pypi
perl                      5.32.1          7_h10d778d_perl5    conda-forge
pexpect                   4.9.0              pyhd8ed1ab_0    conda-forge
phonopy                   2.22.1                   pypi_0    pypi
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    10.2.0          py311hea5c87a_0    conda-forge
pint                      0.23               pyhd8ed1ab_0    conda-forge
pip                       24.0               pyhd8ed1ab_0    conda-forge
pixman                    0.43.4               h73e2aa4_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_1    conda-forge
platformdirs              4.2.0              pyhd8ed1ab_0    conda-forge
plotly                    5.22.0                   pypi_0    pypi
pluggy                    1.4.0              pyhd8ed1ab_0    conda-forge
pre-commit                3.7.0                    pypi_0    pypi
prometheus_client         0.20.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.42             pyha770c72_0    conda-forge
prompt_toolkit            3.0.42               hd8ed1ab_0    conda-forge
protobuf                  4.25.3          py311h01b5fa2_0    conda-forge
psi4                      1.9.1           py311h5db8dd7_1    conda-forge
psutil                    5.9.8           py311he705e18_0    conda-forge
pthread-stubs             0.4               hc929b4f_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pubchempy                 1.0.4                    pypi_0    pypi
pugixml                   1.14                 he965462_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
py-cpuinfo                9.0.0              pyhd8ed1ab_0    conda-forge
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pybtex                    0.24.0                   pypi_0    pypi
pycairo                   1.26.0          py311h389a0fd_0    conda-forge
pycalverter               1.6.1                      py_0    conda-forge
pycosat                   0.6.6           py311h2725bcf_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pydantic                  1.10.14         py311he705e18_0    conda-forge
pydantic-core             2.16.3          py311hd64b9fd_0    conda-forge
pydantic-settings         2.2.1                    pypi_0    pypi
pydash                    8.0.0                    pypi_0    pypi
pyedr                     0.8.0              pyhd8ed1ab_0    conda-forge
pygments                  2.17.2             pyhd8ed1ab_0    conda-forge
pyjwt                     2.8.0              pyhd8ed1ab_1    conda-forge
pymatgen                  2024.5.1                 pypi_0    pypi
pymatgen-analysis-alloys  0.0.6                    pypi_0    pypi
pymatgen-analysis-diffusion 2023.8.15                pypi_0    pypi
pymbar                    3.1.1           py311he5d6b3b_3    conda-forge
pymongo                   4.6.3           py311hdd0406b_0    conda-forge
pymsmt                    22.0                     pypi_0    pypi
pynacl                    1.5.0           py311h2725bcf_3    conda-forge
pyobjc-core               10.2            py311h9b70068_0    conda-forge
pyobjc-framework-cocoa    10.2            py311h9b70068_0    conda-forge
pyparsing                 3.1.2              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
pytables                  3.9.2           py311h3cee394_1    conda-forge
pytest                    7.4.4              pyhd8ed1ab_0    conda-forge
python                    3.11.8          h9f0c242_0_cpython    conda-forge
python-constraint         1.4.0                      py_0    conda-forge
python-dateutil           2.9.0.post0              pypi_0    pypi
python-dotenv             1.0.1                    pypi_0    pypi
python-fastjsonschema     2.19.1             pyhd8ed1ab_0    conda-forge
python-igraph             0.11.4          py311h090a316_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python-multipart          0.0.9              pyhd8ed1ab_0    conda-forge
python-symengine          0.11.0          py311h0d02041_1    conda-forge
python-tzdata             2024.1             pyhd8ed1ab_0    conda-forge
python_abi                3.11                    4_cp311    conda-forge
pytng                     0.3.1           py311h0c3a6a7_1    conda-forge
pytorch-lightning         2.2.1                    pypi_0    pypi
pytraj                    2.0.6                    pypi_0    pypi
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.1           py311h2725bcf_1    conda-forge
pyzmq                     25.1.2          py311h889d6d6_0    conda-forge
qcelemental               0.27.1             pyhd8ed1ab_0    conda-forge
qcengine                  0.29.0             pyhd8ed1ab_0    conda-forge
qcportal                  0.55               pyhd8ed1ab_0    conda-forge
rdkit                     2023.09.6       py311hc8a6178_0    conda-forge
readline                  8.2                  h9e318b2_1    conda-forge
redis-py                  5.0.4              pyhd8ed1ab_0    conda-forge
redis-server              7.2.5                h2d65c12_0    conda-forge
referencing               0.34.0             pyhd8ed1ab_0    conda-forge
regex                     2024.5.15       py311h72ae277_0    conda-forge
reportlab                 4.1.0           py311he705e18_0    conda-forge
reproc                    14.2.4.post0         h10d778d_1    conda-forge
reproc-cpp                14.2.4.post0         h93d8f39_1    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rich                      13.7.1             pyhd8ed1ab_0    conda-forge
rlpycairo                 0.2.0              pyhd8ed1ab_0    conda-forge
robocrys                  0.2.8                    pypi_0    pypi
rpds-py                   0.18.0          py311hd64b9fd_0    conda-forge
ruamel-yaml               0.17.40                  pypi_0    pypi
ruamel.yaml               0.18.6          py311he705e18_0    conda-forge
ruamel.yaml.clib          0.2.8           py311he705e18_0    conda-forge
ruff                      0.4.3                    pypi_0    pypi
s3transfer                0.10.1             pyhd8ed1ab_0    conda-forge
sander                    22.0                     pypi_0    pypi
scikit-learn              1.4.1.post1     py311he2b4599_0    conda-forge
scipy                     1.12.0          py311h86d0cd9_2    conda-forge
seaborn                   0.13.2               hd8ed1ab_0    conda-forge
seaborn-base              0.13.2             pyhd8ed1ab_0    conda-forge
seekpath                  2.1.0                    pypi_0    pypi
send2trash                1.8.2              pyhd1c38e8_0    conda-forge
sentinels                 1.0.0                    pypi_0    pypi
setuptools                69.2.0             pyhd8ed1ab_0    conda-forge
shapely                   2.0.3                    pypi_0    pypi
shellingham               1.5.4              pyhd8ed1ab_0    conda-forge
simple-dftd3              1.0.0                h16f0d12_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
smirnoff99frosst          1.1.0              pyh44b312d_0    conda-forge
snappy                    1.1.10               h225ccf5_0    conda-forge
sniffio                   1.3.1              pyhd8ed1ab_0    conda-forge
solvation-analysis        0.1.5+196.g9b83862.dirty          pypi_0    pypi
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
spglib                    2.3.1                    pypi_0    pypi
sqlalchemy                2.0.29          py311he705e18_0    conda-forge
sqlite                    3.45.2               h7461747_0    conda-forge
sshtunnel                 0.4.0                    pypi_0    pypi
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
starlette                 0.36.3                   pypi_0    pypi
statsmodels               0.14.1          py311hc9a392d_0    conda-forge
symengine                 0.11.2               h29729e3_1    conda-forge
sympy                     1.12            pypyh9d50eac_103    conda-forge
tabulate                  0.9.0              pyhd8ed1ab_1    conda-forge
tbb                       2021.12.0            h3c5361c_1    conda-forge
tenacity                  8.2.3                    pypi_0    pypi
terminado                 0.18.1             pyh31c8845_0    conda-forge
texttable                 1.7.0              pyhd8ed1ab_0    conda-forge
threadpoolctl             3.4.0              pyhc1e730c_0    conda-forge
tidynamics                1.1.2              pyhd8ed1ab_0    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.13               h1abcd95_1    conda-forge
toml-f                    0.4.2                he7e6219_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
torch                     2.2.2                    pypi_0    pypi
torchdata                 0.7.1                    pypi_0    pypi
torchmetrics              1.3.2                    pypi_0    pypi
tornado                   6.4             py311he705e18_0    conda-forge
torsiondrive              1.1.0              pyhd8ed1ab_0    conda-forge
tqdm                      4.66.2             pyhd8ed1ab_0    conda-forge
traitlets                 5.14.2             pyhd8ed1ab_0    conda-forge
truststore                0.8.0              pyhd8ed1ab_0    conda-forge
typer                     0.12.3             pyhd8ed1ab_0    conda-forge
typer-slim                0.12.3             pyhd8ed1ab_0    conda-forge
typer-slim-standard       0.12.3               hd8ed1ab_0    conda-forge
types-python-dateutil     2.9.0.20240316     pyhd8ed1ab_0    conda-forge
typing-extensions         4.10.0               hd8ed1ab_0    conda-forge
typing_extensions         4.10.0             pyha770c72_0    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge
tzdata                    2024a                h0c530f3_0    conda-forge
ujson                     5.10.0          py311hbafa61a_0    conda-forge
uncertainties             3.1.7                    pypi_0    pypi
unidecode                 1.3.8              pyhd8ed1ab_0    conda-forge
unyt                      2.9.2              pyhd8ed1ab_1    conda-forge
uri-template              1.3.0              pyhd8ed1ab_0    conda-forge
urllib3                   2.2.1              pyhd8ed1ab_0    conda-forge
uvicorn                   0.29.0                   pypi_0    pypi
vine                      5.1.0              pyhd8ed1ab_0    conda-forge
virtualenv                20.25.1                  pypi_0    pypi
waterdynamics             1.1.0                    pypi_0    pypi
wcwidth                   0.2.13             pyhd8ed1ab_0    conda-forge
webcolors                 1.13               pyhd8ed1ab_0    conda-forge
webencodings              0.5.1              pyhd8ed1ab_2    conda-forge
websocket-client          1.7.0              pyhd8ed1ab_0    conda-forge
werkzeug                  3.0.1              pyhd8ed1ab_0    conda-forge
wheel                     0.43.0             pyhd8ed1ab_1    conda-forge
widgetsnbextension        4.0.10             pyhd8ed1ab_0    conda-forge
wrapt                     1.16.0          py311he705e18_0    conda-forge
xmltodict                 0.13.0             pyhd8ed1ab_0    conda-forge
xorg-kbproto              1.0.7             h35c211d_1002    conda-forge
xorg-libice               1.1.1                h0dc2134_0    conda-forge
xorg-libsm                1.2.4                h0dc2134_0    conda-forge
xorg-libx11               1.8.7                hbd0b022_0    conda-forge
xorg-libxau               1.0.11               h0dc2134_0    conda-forge
xorg-libxdmcp             1.1.3                h35c211d_0    conda-forge
xorg-libxext              1.3.4                hb7f2c08_2    conda-forge
xorg-libxt                1.3.0                h0dc2134_1    conda-forge
xorg-xextproto            7.3.0             hb7f2c08_1003    conda-forge
xorg-xproto               7.0.31            h35c211d_1007    conda-forge
xtb                       6.5.1                h5bf119a_1    conda-forge
xtb-python                22.1            py311h5547dcb_0    conda-forge
xz                        5.2.6                h775f41a_0    conda-forge
yaml                      0.2.5                h0d85af4_2    conda-forge
yaml-cpp                  0.8.0                he965462_0    conda-forge
yarl                      1.9.4                    pypi_0    pypi
zeromq                    4.3.5                h93d8f39_0    conda-forge
zipp                      3.17.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               h8a1eda9_5    conda-forge
zlib-ng                   2.0.7                hb7f2c08_0    conda-forge
zstandard                 0.22.0          py311hed14148_0    conda-forge
zstd                      1.5.5                h829000d_0    conda-forge

[j-wags]

I just retried with a new env on an M1 macbook and the command from your original post completed for me. Could you check this with a newly-built env and let me know if it completes? That will help determine if it's your system or conda env that's the issue.

[orionarcher]

Yep will do in the next few days. Thanks for checking it out.