ConnectTimeout error without sufficient information to trace the cause of the issue #417
Description
Description
I am trying to parametrize a simple MMA-MMA dimer with bespokefit. I have created the following mma-mma-dimer-obabel.sdf file,
mma-mma-dimer.pdb
OpenBabel12052518203D
38 37 0 0 1 0 0 0 0 0999 V2000
1.1540 0.0040 0.1790 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2610 -0.3340 -0.3230 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3110 1.5400 0.1510 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1630 -0.6840 -0.7600 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2560 0.7740 -0.5710 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.6510 -1.7720 -0.5760 O 0 0 0 0 0 0 0 0 0 0 0 0
0.4570 2.0040 0.7470 H 0 0 0 0 0 0 0 0 0 0 0 0
1.2240 1.8750 -0.9350 H 0 0 0 0 0 0 0 0 0 0 0 0
3.2280 -0.4910 -0.4180 H 0 0 0 0 0 0 0 0 0 0 0 0
1.9720 -1.8090 -0.7510 H 0 0 0 0 0 0 0 0 0 0 0 0
2.0260 -0.2860 -1.8200 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.6200 0.3290 -0.1030 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.9300 -0.6040 -0.6800 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.5790 0.0900 1.0120 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.3760 1.1610 -0.2880 H 0 0 0 0 0 0 0 0 0 0 0 0
2.6320 2.0880 0.7340 C 0 0 2 0 0 0 0 0 0 0 0 0
2.7120 1.8350 2.2500 C 0 0 0 0 0 0 0 0 0 0 0 0
2.6320 3.6130 0.5300 C 0 0 0 0 0 0 0 0 0 0 0 0
3.8700 1.4920 0.0430 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4460 1.6570 3.0520 O 0 0 0 0 0 0 0 0 0 0 0 0
4.0570 1.7310 2.9280 O 0 0 0 0 0 0 0 0 0 0 0 0
2.5600 3.8550 -0.5820 H 0 0 0 0 0 0 0 0 0 0 0 0
3.5910 4.0560 0.9580 H 0 0 0 0 0 0 0 0 0 0 0 0
3.8150 1.6860 -1.0790 H 0 0 0 0 0 0 0 0 0 0 0 0
4.8080 1.9790 0.4700 H 0 0 0 0 0 0 0 0 0 0 0 0
3.9170 0.3730 0.2470 H 0 0 0 0 0 0 0 0 0 0 0 0
1.6660 2.1880 4.4470 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5310 1.6250 4.9340 H 0 0 0 0 0 0 0 0 0 0 0 0
1.9180 3.2980 4.3940 H 0 0 0 0 0 0 0 0 0 0 0 0
0.7190 2.0410 5.0640 H 0 0 0 0 0 0 0 0 0 0 0 0
1.3200 -0.5530 1.6030 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1710 -1.6830 1.5880 H 0 0 0 0 0 0 0 0 0 0 0 0
2.3680 -0.3110 1.9840 H 0 0 0 0 0 0 0 0 0 0 0 0
0.5450 -0.0780 2.2900 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4170 4.1970 1.2740 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3980 5.3290 1.1450 H 0 0 0 0 0 0 0 0 0 0 0 0
0.4610 3.7460 0.8470 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4950 3.9400 2.3830 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 4 1 0 0 0 0
1 3 1 0 0 0 0
1 31 1 0 0 0 0
2 5 1 0 0 0 0
2 6 2 0 0 0 0
3 7 1 0 0 0 0
3 8 1 0 0 0 0
3 16 1 0 0 0 0
4 9 1 0 0 0 0
4 10 1 0 0 0 0
4 11 1 0 0 0 0
5 12 1 0 0 0 0
12 13 1 0 0 0 0
12 14 1 0 0 0 0
12 15 1 0 0 0 0
16 17 1 1 0 0 0
16 19 1 0 0 0 0
16 18 1 0 0 0 0
17 20 1 0 0 0 0
17 21 2 0 0 0 0
18 22 1 0 0 0 0
18 23 1 0 0 0 0
18 35 1 0 0 0 0
19 24 1 0 0 0 0
19 25 1 0 0 0 0
19 26 1 0 0 0 0
20 27 1 0 0 0 0
27 28 1 0 0 0 0
27 29 1 0 0 0 0
27 30 1 0 0 0 0
31 32 1 0 0 0 0
31 33 1 0 0 0 0
31 34 1 0 0 0 0
35 36 1 0 0 0 0
35 37 1 0 0 0 0
35 38 1 0 0 0 0
M END
> <REMARK>
Materials Studio PDB file
Created: Thu Dec 04 07:57:12 Tokyo Standard Time 2025
$$$$
and, following the quick-start guide at https://docs.openforcefield.org/projects/bespokefit/en/stable/getting-started/quick-start.html#using-the-api, I have generated a default workflow bespoke_workflow.json,
{
"initial_force_field": "openff-2.2.0.offxml",
"optimizer": {
"type": "ForceBalance",
"max_iterations": 10,
"job_type": "optimize",
"penalty_type": "L2",
"step_convergence_threshold": 0.01,
"objective_convergence_threshold": 0.01,
"gradient_convergence_threshold": 0.01,
"n_criteria": 2,
"eigenvalue_lower_bound": 0.01,
"finite_difference_h": 0.01,
"penalty_additive": 1.0,
"initial_trust_radius": -0.25,
"minimum_trust_radius": 0.05,
"error_tolerance": 1.0,
"adaptive_factor": 0.2,
"adaptive_damping": 1.0,
"normalize_weights": false,
"extras": {}
},
"target_templates": [
{
"weight": 1.0,
"reference_data": null,
"calculation_specification": null,
"extras": {},
"type": "TorsionProfile",
"attenuate_weights": true,
"energy_denominator": 1.0,
"energy_cutoff": 10.0
}
],
"parameter_hyperparameters": [
{
"type": "ProperTorsions",
"priors": {
"k": 6.0
}
}
],
"target_torsion_smirks": [
"[!#1]~[!$(*#*)&!D1:1]-,=;!@[!$(*#*)&!D1:2]~[!#1]"
],
"smirk_settings": {
"expand_torsion_terms": true,
"generate_bespoke_terms": true
},
"fragmentation_engine": {
"functional_groups": {
"hydrazine": "[NX3:1][NX3:2]",
"hydrazone": "[NX3:1][NX2:2]",
"nitric_oxide": "[N:1]-[O:2]",
"amide": "[#7:1][#6:2](=[#8:3])",
"amide_n": "[#7:1][#6:2](-[O-:3])",
"amide_2": "[NX3:1][CX3:2](=[OX1:3])[NX3:4]",
"aldehyde": "[CX3H1:1](=[O:2])[#6:3]",
"sulfoxide_1": "[#16X3:1]=[OX1:2]",
"sulfoxide_2": "[#16X3+:1][OX1-:2]",
"sulfonyl": "[#16X4:1](=[OX1:2])=[OX1:3]",
"sulfinic_acid": "[#16X3:1](=[OX1:2])[OX2H,OX1H0-:3]",
"sulfinamide": "[#16X4:1](=[OX1:2])(=[OX1:3])([NX3R0:4])",
"sulfonic_acid": "[#16X4:1](=[OX1:2])(=[OX1:3])[OX2H,OX1H0-:4]",
"phosphine_oxide": "[PX4:1](=[OX1:2])([#6:3])([#6:4])([#6:5])",
"phosphonate": "[P:1](=[OX1:2])([OX2H,OX1-:3])([OX2H,OX1-:4])",
"phosphate": "[PX4:1](=[OX1:2])([#8:3])([#8:4])([#8:5])",
"carboxylic_acid": "[CX3:1](=[O:2])[OX1H0-,OX2H1:3]",
"nitro_1": "[NX3+:1](=[O:2])[O-:3]",
"nitro_2": "[NX3:1](=[O:2])=[O:3]",
"ester": "[CX3:1](=[O:2])[OX2H0:3]",
"tri_halide": "[#6:1]([F,Cl,I,Br:2])([F,Cl,I,Br:3])([F,Cl,I,Br:4])"
},
"scheme": "WBO",
"wbo_options": {
"method": "am1-wiberg-elf10",
"max_conformers": 800,
"rms_threshold": 1.0
},
"threshold": 0.03,
"heuristic": "path_length",
"keep_non_rotor_ring_substituents": false
},
"default_qc_specs": [
{
"method": "B3LYP-D3BJ",
"basis": "DZVP",
"program": "psi4",
"spec_name": "default",
"spec_description": "Standard OpenFF optimization quantum chemistry specification.",
"store_wavefunction": "none",
"implicit_solvent": null,
"maxiter": 200,
"scf_properties": [
"dipole",
"quadrupole",
"wiberg_lowdin_indices",
"mayer_indices"
],
"keywords": {}
}
]
}Now, I run bespokefit with
openff-bespoke executor run --file mma-mma-dimer-obabel.sdf \
--workflow-file bespoke_workflow.json \
--output "mma-mma-dimer.json" \
--output-force-field "mma-mma-dimer.offxml" \
--n-qc-compute-workers 2 \
--qc-compute-n-cores 1 \
--default-qc-spec xtb gfn2xtb noneFragmentation succeeds, but then I get this cryptic error that I don't know how to interpret,
$ openff-bespoke executor run --file mma-mma-dimer-obabel.sdf \
> --workflow-file bespoke_workflow.json \
> --output "mma-mma-dimer.json" \
> --output-force-field "mma-mma-dimer.offxml" \
> --n-qc-compute-workers 2 \
> --qc-compute-n-cores 1 \
> --default-qc-spec xtb gfn2xtb none
/home/hoermann/miniforge3/envs/bespokefit-env/lib/python3.12/site-packages/smirnoff99frosst/smirnoff99frosst.py:11: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
from pkg_resources import resource_filename
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── 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[C@](C)(CC(C)(C)C(=O)OC)C(=O)OC │ mma-mma-dimer.pdb │ mma-mma-dimer-obabel.sdf │
└────┴───────────────────────────────────┴───────────────────┴──────────────────────────┘
3. running the fitting pipeline
[✓] fragmentation successful
[x] qc-generation failed
"ConnectTimeout: "
outputs have been saved to mma-mma-dimer.json
worker: Warm shutdown (MainProcess)
ERROR:openff.bespokefit.executor.services.coordinator.app:Exception raised by the main loop. This should never happen.
Traceback (most recent call last):
File "/home/hoermann/miniforge3/envs/bespokefit-env/lib/python3.12/site-packages/openff/bespokefit/executor/services/coordinator/app.py", line 175, in _handle_task_result
task.result()
File "/home/hoermann/miniforge3/envs/bespokefit-env/lib/python3.12/site-packages/openff/bespokefit/executor/services/coordinator/worker.py", line 84, in cycle
push_task_status(
File "/home/hoermann/miniforge3/envs/bespokefit-env/lib/python3.12/site-packages/openff/bespokefit/executor/services/coordinator/storage.py", line 127, in push_task_status
return connection.rpush(_QUEUE_NAMES[status], task_id)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/hoermann/miniforge3/envs/bespokefit-env/lib/python3.12/site-packages/redis/commands/core.py", line 3001, in rpush
return self.execute_command("RPUSH", name, *values)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/hoermann/miniforge3/envs/bespokefit-env/lib/python3.12/site-packages/redis/client.py", line 657, in execute_command
return self._execute_command(*args, **options)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/hoermann/miniforge3/envs/bespokefit-env/lib/python3.12/site-packages/redis/client.py", line 668, in _execute_command
return conn.retry.call_with_retry(
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/hoermann/miniforge3/envs/bespokefit-env/lib/python3.12/site-packages/redis/retry.py", line 116, in call_with_retry
return do()
^^^^
File "/home/hoermann/miniforge3/envs/bespokefit-env/lib/python3.12/site-packages/redis/client.py", line 669, in <lambda>
lambda: self._send_command_parse_response(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/hoermann/miniforge3/envs/bespokefit-env/lib/python3.12/site-packages/redis/client.py", line 639, in _send_command_parse_response
conn.send_command(*args, **options)
File "/home/hoermann/miniforge3/envs/bespokefit-env/lib/python3.12/site-packages/redis/connection.py", line 1097, in send_command
self._command_packer.pack(*args),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/hoermann/miniforge3/envs/bespokefit-env/lib/python3.12/site-packages/redis/connection.py", line 134, in pack
for arg in map(self.encode, args):
^^^^^^^^^^^^^^^^^^^^^^
File "/home/hoermann/miniforge3/envs/bespokefit-env/lib/python3.12/site-packages/redis/_parsers/encoders.py", line 29, in encode
raise DataError(
redis.exceptions.DataError: Invalid input of type: 'NoneType'. Convert to a bytes, string, int or float first.
ERROR:openff.bespokefit.executor.services.coordinator.app:Exception raised by the main loop. This should never happen.
Traceback (most recent call last):
File "/home/hoermann/miniforge3/envs/bespokefit-env/lib/python3.12/site-packages/openff/bespokefit/executor/services/coordinator/app.py", line 175, in _handle_task_result
task.result()
File "/home/hoermann/miniforge3/envs/bespokefit-env/lib/python3.12/site-packages/openff/bespokefit/executor/services/coordinator/worker.py", line 84, in cycle
push_task_status(
File "/home/hoermann/miniforge3/envs/bespokefit-env/lib/python3.12/site-packages/openff/bespokefit/executor/services/coordinator/storage.py", line 127, in push_task_status
return connection.rpush(_QUEUE_NAMES[status], task_id)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/hoermann/miniforge3/envs/bespokefit-env/lib/python3.12/site-packages/redis/commands/core.py", line 3001, in rpush
return self.execute_command("RPUSH", name, *values)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/hoermann/miniforge3/envs/bespokefit-env/lib/python3.12/site-packages/redis/client.py", line 657, in execute_command
return self._execute_command(*args, **options)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/hoermann/miniforge3/envs/bespokefit-env/lib/python3.12/site-packages/redis/client.py", line 668, in _execute_command
return conn.retry.call_with_retry(
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/hoermann/miniforge3/envs/bespokefit-env/lib/python3.12/site-packages/redis/retry.py", line 116, in call_with_retry
return do()
^^^^
File "/home/hoermann/miniforge3/envs/bespokefit-env/lib/python3.12/site-packages/redis/client.py", line 669, in <lambda>
lambda: self._send_command_parse_response(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/hoermann/miniforge3/envs/bespokefit-env/lib/python3.12/site-packages/redis/client.py", line 639, in _send_command_parse_response
conn.send_command(*args, **options)
File "/home/hoermann/miniforge3/envs/bespokefit-env/lib/python3.12/site-packages/redis/connection.py", line 1097, in send_command
self._command_packer.pack(*args),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/hoermann/miniforge3/envs/bespokefit-env/lib/python3.12/site-packages/redis/connection.py", line 134, in pack
for arg in map(self.encode, args):
^^^^^^^^^^^^^^^^^^^^^^
File "/home/hoermann/miniforge3/envs/bespokefit-env/lib/python3.12/site-packages/redis/_parsers/encoders.py", line 29, in encode
raise DataError(
redis.exceptions.DataError: Invalid input of type: 'NoneType'. Convert to a bytes, string, int or float first.
worker: Warm shutdown (MainProcess)
I would appreciate some help with finding and fixing the cause of this issue.
Thank you very much.
Software versions
- Which operating system and version are you using? CentOS 7
- How did you install BespokeFit? With mamba, as described on https://docs.openforcefield.org/projects/bespokefit/en/latest/getting-started/installation.html. I have, however, installed the current development version of bespokefit from github.
- Are you using Apple Silicon? If so, are you running BespokeFit in Rosetta or directly? No
- What is the output of running
conda list?
Output of conda list
# packages in environment at /home/hoermann/miniforge3/envs/bespokefit-env: # # Name Version Build Channel _openmp_mutex 4.5 7_kmp_llvm conda-forge _python_abi3_support 1.0 hd8ed1ab_2 conda-forge ambertools 24.8 cuda_None_nompi_py312hbe1986e_101 conda-forge amberutils 21.0 pypi_0 pypi amqp 5.2.0 pyhd8ed1ab_2 conda-forge annotated-doc 0.0.4 pyhcf101f3_0 conda-forge anyio 4.12.0 pyhcf101f3_0 conda-forge apsw 3.51.1.0 py312h4c3975b_0 conda-forge argcomplete 3.6.3 pyhd8ed1ab_0 conda-forge argon2-cffi 25.1.0 pyhd8ed1ab_0 conda-forge argon2-cffi-bindings 25.1.0 py312h4c3975b_2 conda-forge arpack 3.9.1 nompi_hf03ea27_102 conda-forge arrow 1.4.0 pyhcf101f3_0 conda-forge asttokens 3.0.1 pyhd8ed1ab_0 conda-forge async-lru 2.0.5 pyh29332c3_0 conda-forge async-timeout 5.0.1 pyhd8ed1ab_1 conda-forge attrs 25.4.0 pyhcf101f3_1 conda-forge babel 2.17.0 pyhd8ed1ab_0 conda-forge basis_set_exchange 0.11 pyhd8ed1ab_0 conda-forge beautifulsoup4 4.14.3 pyha770c72_0 conda-forge billiard 4.2.4 py312h4c3975b_0 conda-forge bleach 6.3.0 pyhcf101f3_0 conda-forge bleach-with-css 6.3.0 h5f6438b_0 conda-forge blosc 1.21.6 he440d0b_1 conda-forge boto3 1.42.3 pyhd8ed1ab_0 conda-forge botocore 1.42.3 pyhd8ed1ab_0 conda-forge brotli 1.2.0 hed03a55_1 conda-forge brotli-bin 1.2.0 hb03c661_1 conda-forge brotli-python 1.2.0 py312hdb49522_1 conda-forge bson 0.5.10 pyhd8ed1ab_0 conda-forge bzip2 1.0.8 hda65f42_8 conda-forge c-ares 1.34.5 hb9d3cd8_0 conda-forge c-blosc2 2.22.0 hc31b594_1 conda-forge ca-certificates 2025.11.12 hbd8a1cb_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cachetools 6.2.2 pyhd8ed1ab_0 conda-forge cairo 1.18.4 h3394656_0 conda-forge celery 5.5.3 pyhe01879c_0 conda-forge certifi 2025.11.12 pyhd8ed1ab_0 conda-forge cffi 2.0.0 py312h460c074_1 conda-forge charset-normalizer 3.4.4 pyhd8ed1ab_0 conda-forge chemper 1.0.1 pyhd8ed1ab_0 conda-forge click 8.3.1 pyh8f84b5b_1 conda-forge click-didyoumean 0.3.1 pyhd8ed1ab_1 conda-forge 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