xtb Compute for the fragmented ligand set. #146

jthorton · 2020-10-12T14:03:52Z

Created a new folder in the submissions directory containing the dataset
Added README.md describing the dataset see here for examples
All files used to produce the dataset are included with a description
Dataset follows the QCSubmit schema defined for Datasets, OptimizationDatasets and TorsionDriveDatasets
Dataset is named dataset.json
A PDF depicting the molecules is attached, in the case of torsiondrives this should include the highlighting of the central bond, this can be done automatically using qcsubmit.
QCSubmit validation passed
Ready to submit!

This PR adds an xtb compute JSON which expands the fragmented benchmark ligands set.

openff-dangerbot · 2020-10-12T14:09:26Z

QCSubmit Validation Report

QC Specification Report

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.152.g76dd8ac
openforcefield	0.7.2
basis_set_exchange	v0.8.12
qcelemental	v0.17.0
openeye	2020.1.0

openff-dangerbot · 2020-10-12T14:24:54Z

QCSubmit Validation Report

QC Specification Report

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.152.g76dd8ac
openforcefield	0.7.2
basis_set_exchange	v0.8.12
qcelemental	v0.17.0
openeye	2020.1.0

openff-dangerbot · 2020-10-12T14:33:53Z

QCSubmit Validation Report

	submissions/2020-07-27-OpenFF-Benchmark-Ligands/compute_xtb.json
Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
Elements	H ,S ,O ,Br ,F ,C ,Cl ,I ,N
Valid Cmiles	✔️
Connected Dihedrals	✔️
No Linear Torsions	✔️
No Molecular Complexes	✔️
Valid Constraints	✔️
Complete Metatdata	✔️
Valid SCF Properties	✔️

QC Specification Report

	submissions/2020-07-27-OpenFF-Benchmark-Ligands/compute_xtb.json/gfn2xtb	submissions/2020-07-27-OpenFF-Benchmark-Ligands/compute_xtb.json/gfn1xtb	submissions/2020-07-27-OpenFF-Benchmark-Ligands/compute_xtb.json/gfnff
Specification Name	gfn2xtb	gfn1xtb	gfnff
Method	gfn2xtb	gfn1xtb	gfnff
Basis
Wavefunction Protocol	none	none	none
Validated	✔️	✔️	✔️
Full Basis Coverage	✔️	✔️	✔️

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.152.g76dd8ac
openforcefield	0.7.2
basis_set_exchange	v0.8.12
qcelemental	v0.17.0
openeye	2020.1.0

jthorton · 2020-10-12T14:41:59Z

@dotsdl @trevorgokey this should be good to go I just want to make sure we have some xtb workers ready for this it should be quite fast.

dotsdl · 2020-10-13T17:12:04Z

Reviewing now, thanks for putting this together @jthorton!

dotsdl

Looks great @jthorton! Feel free to merge when ready!

openff-dangerbot · 2020-10-14T08:59:53Z

Lifecycle - QCSubmit Submission Report : SUCCESS


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-10-14 08:59 UTC

Response from public QCArchive:

{'gfn2xtb': 481, 'gfn1xtb': 481, 'gfnff': 481}

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.152.g76dd8ac
openforcefield	0.7.2
basis_set_exchange	v0.8.12
qcelemental	v0.17.0
openeye	2020.1.0

openff-dangerbot · 2020-10-14T12:33:09Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-10-14 12:33 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	INCOMPLETE	ERROR
gfn2xtb	0	0	481	0
gfn1xtb	0	0	481	0
gfnff	0	0	481	0

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	0	0	0
gfn1xtb	0	0	0
gfnff	0	0	0

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.152.g76dd8ac
openforcefield	0.7.2
basis_set_exchange	v0.8.12
qcelemental	v0.17.0
openeye	2020.1.0

dotsdl · 2020-10-14T23:05:19Z

I can spin up some xtb workers on PRP to see how this fares. I'll start a small number to see if we're getting reasonable results.

openff-dangerbot · 2020-10-15T12:33:47Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-10-15 12:33 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	RUNNING	INCOMPLETE
gfn2xtb	50	431
gfn1xtb	0	481
gfnff	0	481

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
gfn2xtb	655	281
gfn1xtb	0	0
gfnff	0	0

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.152.g76dd8ac
openforcefield	0.7.2
basis_set_exchange	v0.8.12
qcelemental	v0.17.0
openeye	2020.1.0

openff-dangerbot · 2020-10-16T12:45:05Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-10-16 12:45 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	INCOMPLETE
gfn2xtb	5	130	346
gfn1xtb	0	0	481
gfnff	0	0	481

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
gfn2xtb	2405	673
gfn1xtb	0	0
gfnff	0	0

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.222.g3eb3978
openforcefield	0.7.2
basis_set_exchange	v0.8.12
qcelemental	v0.17.0
rdkit	2020.03.6

openff-dangerbot · 2020-10-17T12:32:18Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-10-17 12:32 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	INCOMPLETE
gfn2xtb	7	128	346
gfn1xtb	0	0	481
gfnff	0	0	481

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
gfn2xtb	2701	593
gfn1xtb	0	0
gfnff	0	0

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.222.g3eb3978
openforcefield	0.7.2
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.03.6

openff-dangerbot · 2020-10-19T02:12:14Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-10-19 02:12 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	INCOMPLETE	ERROR
gfn2xtb	7	127	346	1
gfn1xtb	0	0	481	0
gfnff	0	0	481	0

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	3075	590	1
gfn1xtb	0	0	0
gfnff	0	0	0

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 1

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1299, in optimizeGeometry
self.evaluateStep()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1277, in evaluateStep
Eig1 = np.linalg.eigh(self.H)[0]
File "<__array_function__ internals>", line 6, in eigh
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 1471, in eigh
w, vt = gufunc(a, signature=signature, extobj=extobj)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 94, in _raise_linalgerror_eigenvalues_nonconvergence
raise LinAlgError("Eigenvalues did not converge")
numpy.linalg.LinAlgError: Eigenvalues did not converge


ids :
{'25835577'}
-------------------------------------

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.222.g3eb3978
openforcefield	0.7.2
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.03.6

openff-dangerbot · 2020-10-19T12:35:22Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-10-19 12:35 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	INCOMPLETE
gfn2xtb	7	128	346
gfn1xtb	0	0	481
gfnff	0	0	481

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
gfn2xtb	3075	591
gfn1xtb	0	0
gfnff	0	0

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.222.g3eb3978
openforcefield	0.7.2
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.03.6

openff-dangerbot · 2020-10-20T12:34:14Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-10-20 12:34 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	INCOMPLETE	ERROR
gfn2xtb	10	124	346	1
gfn1xtb	0	0	481	0
gfnff	0	0	481	0

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	3529	488	1
gfn1xtb	0	0	0
gfnff	0	0	0

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 1

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1299, in optimizeGeometry
self.evaluateStep()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1277, in evaluateStep
Eig1 = np.linalg.eigh(self.H)[0]
File "<__array_function__ internals>", line 6, in eigh
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 1471, in eigh
w, vt = gufunc(a, signature=signature, extobj=extobj)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 94, in _raise_linalgerror_eigenvalues_nonconvergence
raise LinAlgError("Eigenvalues did not converge")
numpy.linalg.LinAlgError: Eigenvalues did not converge


ids :
{'25835577'}
-------------------------------------

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.222.g3eb3978
openforcefield	0.7.2
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.03.6

openff-dangerbot · 2020-10-21T12:35:24Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-10-21 12:35 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	INCOMPLETE	ERROR
gfn2xtb	12	279	189	1
gfn1xtb	0	0	481	0
gfnff	0	0	481	0

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	5344	734	1
gfn1xtb	0	0	0
gfnff	0	0	0

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 1

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1299, in optimizeGeometry
self.evaluateStep()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1277, in evaluateStep
Eig1 = np.linalg.eigh(self.H)[0]
File "<__array_function__ internals>", line 6, in eigh
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 1471, in eigh
w, vt = gufunc(a, signature=signature, extobj=extobj)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 94, in _raise_linalgerror_eigenvalues_nonconvergence
raise LinAlgError("Eigenvalues did not converge")
numpy.linalg.LinAlgError: Eigenvalues did not converge


ids :
{'25835577'}
-------------------------------------

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.222.g3eb3978
openforcefield	0.7.2
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.03.6

openff-dangerbot · 2020-10-21T15:37:32Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-10-21 15:37 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	INCOMPLETE	ERROR
gfn2xtb	21	286	173	1
gfn1xtb	0	0	481	0
gfnff	0	0	481	0

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	6130	1328	1
gfn1xtb	0	0	0
gfnff	0	0	0

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 1

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1299, in optimizeGeometry
self.evaluateStep()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1277, in evaluateStep
Eig1 = np.linalg.eigh(self.H)[0]
File "<__array_function__ internals>", line 6, in eigh
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 1471, in eigh
w, vt = gufunc(a, signature=signature, extobj=extobj)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 94, in _raise_linalgerror_eigenvalues_nonconvergence
raise LinAlgError("Eigenvalues did not converge")
numpy.linalg.LinAlgError: Eigenvalues did not converge


ids :
{'25835577'}
-------------------------------------

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.222.g3eb3978
openforcefield	0.7.2
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.03.6

openff-dangerbot · 2020-10-22T12:36:52Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-10-22 12:36 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	INCOMPLETE
gfn2xtb	412	69	0
gfn1xtb	11	252	218
gfnff	0	0	481

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	32026	10	0
gfn1xtb	10302	12	1
gfnff	0	0	0

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 1

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1299, in optimizeGeometry
self.evaluateStep()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1277, in evaluateStep
Eig1 = np.linalg.eigh(self.H)[0]
File "<__array_function__ internals>", line 6, in eigh
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 1471, in eigh
w, vt = gufunc(a, signature=signature, extobj=extobj)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 94, in _raise_linalgerror_eigenvalues_nonconvergence
raise LinAlgError("Eigenvalues did not converge")
numpy.linalg.LinAlgError: Eigenvalues did not converge


ids :
{'27977677'}
-------------------------------------

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.222.g3eb3978
openforcefield	0.7.2
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.03.6

openff-dangerbot · 2020-10-23T13:26:54Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-10-23 13:26 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	INCOMPLETE
gfn2xtb	472	9	0
gfn1xtb	132	342	7
gfnff	0	0	481

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
gfn2xtb	32509	21
gfn1xtb	19695	2003
gfnff	0	0

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.222.g3eb3978
openforcefield	0.7.2
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.03.6

openff-dangerbot · 2020-10-24T12:36:27Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-10-24 12:36 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	INCOMPLETE	ERROR
gfn2xtb	476	5	0	0
gfn1xtb	163	318	0	0
gfnff	0	29	448	4

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	32533	13	0
gfn1xtb	23384	1810	0
gfnff	15	145	23

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 23

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/programs/xtb.py", line 72, in compute
output = run_qcschema(input_data)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/xtb/qcschema/harness.py", line 208, in run_qcschema
return qcel.models.AtomicResult(**ret_data, stdout=output)
File "pydantic/main.py", line 346, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for AtomicResult
return_result
cannot reshape array of size 1 into shape (3) (type=value_error)



ids :
{'28348614', '28348615', '28348616', '28348617', '28348618', '28348619',
'28351111', '28351807', '28351834', '28351835', '28351836', '28351837',
'28351838', '28351839', '28351840', '28351841', '28351842', '28353283',
'28353284', '28353285', '28353286', '28353287', '28353288'}
-------------------------------------

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.222.g3eb3978
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

openff-dangerbot · 2020-10-26T12:39:41Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-10-26 12:39 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	INCOMPLETE	ERROR
gfn2xtb	480	1	0	0
gfn1xtb	363	118	0	0
gfnff	1	182	159	139

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	32575	1	0
gfn1xtb	32375	477	0
gfnff	2513	1188	730

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 701

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/programs/xtb.py", line 72, in compute
output = run_qcschema(input_data)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/xtb/qcschema/harness.py", line 208, in run_qcschema
return qcel.models.AtomicResult(**ret_data, stdout=output)
File "pydantic/main.py", line 346, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for AtomicResult
return_result
cannot reshape array of size 1 into shape (3) (type=value_error)



ids :
{'28348614', '28348615', '28348616', '28348618', '28348619', '28351111',
'28351807', '28351834', '28351835', '28351836', '28351837', '28351838',
'28351839', '28351840', '28351841', '28351842', '28353283', '28353284',
'28353285', '28353286', '28353287', '28353288', '28355916', '28355917',
'28355918', '28355919', '28355920', '28355921', '28363700', '28363701',
'28363702', '28363703', '28363704', '28363705', '28363706', '28363707',
'28363708', '28383947', '28383948', '28383949', '28383950', '28383951',
'28383952', '28383953', '28383954', '28383955', '28383956', '28387068',
'28387069', '28387070', '28387072', '28387073', '28387074', '28387075',
'28389309', '28389310', '28389311', '28389312', '28389314', '28389315',
'28389316', '28394980', '28394981', '28394983', '28394984', '28394985',
'28394986', '28394987', '28394988', '28394989', '28397842', '28397843',
'28397844', '28397845', '28397846', '28397847', '28397848', '28398182',
'28398183', '28398184', '28398185', '28398211', '28398212', '28398622',
'28398623', '28398624', '28398625', '28398626', '28398627', '28477648',
'28477766', '28477803', '28477813', '28477863', '28477932', '28477969',
'28478048', '28478049', '28478092', '28478129', '28478156', '28478157',
'28478158', '28478201', '28478202', '28478248', '28478312', '28478366',
'28478410', '28478412', '28478479', '28478556', '28478672', '28478699',
'28478751', '28478806', '28478822', '28479017', '28479018', '28479064',
'28479075', '28479084', '28479117', '28479118', '28479119', '28479120',
'28496076', '28496077', '28496078', '28496079', '28496080', '28496081',
'28496082', '28496083', '28496134', '28496143', '28496144', '28496165',
'28496175', '28496198', '28496199', '28496200', '28496201', '28496202',
'28510925', '28510926', '28510942', '28510955', '28510974', '28510975',
'28510976', '28510989', '28510990', '28510991', '28510992', '28510993',
'28510994', '28510995', '28510996', '28510997', '28510998', '28511025',
'28511026', '28511030', '28511031', '28511032', '28511039', '28511040',
'28511041', '28511054', '28511055', '28511057', '28511058', '28511059',
'28511071', '28511072', '28511073', '28511074', '28511088', '28511103',
'28511104', '28511114', '28511137', '28511150', '28511161', '28511162',
'28511163', '28511164', '28511179', '28511319', '28511331', '28511332',
'28511333', '28511334', '28511335', '28511337', '28511338', '28511390',
'28511391', '28511392', '28511393', '28511407', '28511416', '28511417',
'28511419', '28511420', '28511433', '28511434', '28511435', '28511451',
'28511457', '28511458', '28511459', '28511462', '28511463', '28511464',
'28511465', '28511466', '28511467', '28511494', '28511557', '28511559',
'28511593', '28511594', '28511595', '28511596', '28511605', '28511614',
'28511616', '28511617', '28511618', '28511619', '28511621', '28511622',
'28511623', '28511624', '28511625', '28520161', '28520202', '28520235',
'28520236', '28520267', '28520268', '28520269', '28520270', '28520271',
'28520272', '28520273', '28520274', '28520275', '28520305', '28520306',
'28520307', '28520308', '28520309', '28520344', '28520348', '28520415',
'28520607', '28520638', '28520669', '28520670', '28520695', '28520705',
'28520737', '28520738', '28520743', '28520771', '28520772', '28520773',
'28520774', '28520775', '28520798', '28520812', '28520813', '28520814',
'28521103', '28521104', '28521105', '28521106', '28521107', '28521108',
'28521109', '28521110', '28521111', '28521112', '28521143', '28521144',
'28521145', '28521146', '28521148', '28521149', '28521150', '28521151',
'28521152', '28521155', '28521165', '28521166', '28521167', '28521168',
'28521169', '28521170', '28521171', '28521172', '28521173', '28521174',
'28521175', '28521176', '28521177', '28521178', '28521179', '28521180',
'28521181', '28521183', '28521184', '28521185', '28521187', '28521188',
'28521189', '28521190', '28521191', '28521192', '28521193', '28521194',
'28521195', '28521196', '28521197', '28521198', '28521199', '28521200',
'28521202', '28521203', '28521204', '28521205', '28521206', '28521207',
'28521208', '28521209', '28521210', '28521211', '28521217', '28521218',
'28521219', '28521220', '28521221', '28521222', '28521223', '28521224',
'28521225', '28521226', '28521227', '28521228', '28521229', '28521230',
'28521231', '28521232', '28521233', '28521234', '28521691', '28521692',
'28521693', '28521694', '28521695', '28521697', '28521698', '28521699',
'28521705', '28521706', '28521707', '28521708', '28521709', '28521710',
'28521735', '28521736', '28521737', '28521738', '28521741', '28521742',
'28521745', '28521746', '28521747', '28521748', '28521749', '28521750',
'28521751', '28521752', '28521753', '28521754', '28521755', '28521756',
'28521757', '28521758', '28521759', '28521760', '28521761', '28521762',
'28521763', '28521764', '28521765', '28521766', '28521767', '28521768',
'28521777', '28521778', '28521779', '28521780', '28521781', '28521782',
'28521783', '28521784', '28521785', '28521786', '28521787', '28521788',
'28521789', '28521790', '28521791', '28521792', '28521793', '28521794',
'28521795', '28521796', '28521797', '28521799', '28521800', '28521801',
'28521802', '28521803', '28521804', '28521805', '28521806', '28521807',
'28521811', '28521812', '28521813', '28521814', '28521815', '28521816',
'28521817', '28521818', '28521819', '28521820', '28521821', '28521822',
'28521823', '28521824', '28521825', '28521826', '28521829', '28521830',
'28521831', '28521832', '28521833', '28521834', '28521835', '28521836',
'28521848', '28521853', '28521854', '28521855', '28521856', '28521857',
'28521858', '28521859', '28521861', '28521862', '28521863', '28521864',
'28521865', '28521866', '28521867', '28521868', '28521869', '28521870',
'28521871', '28521872', '28521873', '28521874', '28521875', '28521876',
'28521877', '28521907', '28521908', '28521909', '28521910', '28521911',
'28521912', '28521913', '28521914', '28521915', '28521937', '28521938',
'28521939', '28521940', '28521941', '28521942', '28521943', '28521944',
'28521945', '28521946', '28521947', '28521948', '28521949', '28521950',
'28521951', '28521952', '28521953', '28521954', '28521955', '28521956',
'28521957', '28521958', '28521959', '28521960', '28521979', '28521980',
'28521981', '28521982', '28521983', '28521984', '28521985', '28521986',
'28521987', '28521988', '28521989', '28521990', '28521991', '28521992',
'28521993', '28521994', '28521995', '28521996', '28521997', '28521998',
'28522000', '28522001', '28522002', '28522003', '28522004', '28522005',
'28522006', '28522007', '28522008', '28522009', '28522011', '28522012',
'28522013', '28522014', '28522015', '28522016', '28522017', '28522018',
'28522019', '28522020', '28522025', '28522026', '28522027', '28522028',
'28522029', '28522030', '28522031', '28522032', '28522033', '28522034',
'28522035', '28522036', '28522037', '28522038', '28522040', '28522041',
'28522042', '28522043', '28522044', '28522045', '28522046', '28522047',
'28522048', '28522049', '28522050', '28522051', '28522052', '28522053',
'28522054', '28522055', '28522056', '28522057', '28522058', '28522059',
'28522060', '28522061', '28522062', '28522064', '28522065', '28522066',
'28522067', '28522068', '28522069', '28522070', '28522071', '28522072',
'28522073', '28522075', '28522076', '28522077', '28522078', '28522079',
'28522080', '28522081', '28522082', '28522083', '28522084', '28522087',
'28522088', '28522089', '28522090', '28522091', '28522092', '28522093',
'28522094', '28522095', '28522096', '28522097', '28522098', '28522099',
'28522100', '28522101', '28522102', '28522103', '28522104', '28522105',
'28522106', '28522118', '28522119', '28522120', '28522121', '28522122',
'28522123', '28522124', '28522125', '28522126', '28522127', '28578707',
'28579455', '28579456', '28579457', '28579458', '28579459', '28579460',
'28579487', '28579825', '28579826', '28580048', '28580049', '28580808',
'28580809', '28580810', '28580811', '28581369', '28581370', '28582537',
'28582538', '28582539', '28584020', '28584021', '28584022', '28584023',
'28584966', '28584967', '28584968', '28584969', '28588765', '28588766',
'28588767', '28589142', '28589143', '28589144', '28589659', '28589660',
'28589661', '28590510', '28593314', '28597880', '28597881', '28600467',
'28600495', '28600498', '28600499', '28600500', '28600501', '28600522',
'28600523', '28600539', '28600540', '28601205', '28601206', '28605809',
'28605810', '28609727', '28609728', '28609729', '28609730'}
-------------------------------------
-------------------------------------
count : 29

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1301, in optimizeGeometry
raise GeomOptNotConvergedError("Optimizer.optimizeGeometry() failed to converge.")
geometric.errors.GeomOptNotConvergedError: Optimizer.optimizeGeometry() failed to converge.


ids :
{'28394045', '28394046', '28394047', '28394048', '28394049', '28394343',
'28394344', '28394345', '28394347', '28394869', '28394909', '28394910',
'28394911', '28394912', '28478411', '28478886', '28478903', '28478978',
'28511180', '28511181', '28511182', '28511183', '28511220', '28511221',
'28511236', '28511237', '28511260', '28511261', '28577775'}
-------------------------------------

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.222.g3eb3978
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

openff-dangerbot · 2020-10-28T09:10:22Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-10-28 09:10 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	ERROR
gfn2xtb	480	1	0
gfn1xtb	478	2	1
gfnff	294	31	156

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	32575	1	0
gfn1xtb	34189	2	1
gfnff	21284	32	904

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 871

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/programs/xtb.py", line 72, in compute
output = run_qcschema(input_data)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/xtb/qcschema/harness.py", line 208, in run_qcschema
return qcel.models.AtomicResult(**ret_data, stdout=output)
File "pydantic/main.py", line 346, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for AtomicResult
return_result
cannot reshape array of size 1 into shape (3) (type=value_error)



ids :
{'28348614', '28348615', '28348616', '28348617', '28348618', '28348619',
'28351111', '28351807', '28351834', '28351835', '28351836', '28351837',
'28351838', '28351839', '28351840', '28351841', '28351842', '28353283',
'28353284', '28353285', '28353286', '28353287', '28353288', '28355916',
'28355917', '28355918', '28355919', '28355920', '28355921', '28363700',
'28363701', '28363702', '28363703', '28363704', '28363705', '28363706',
'28363707', '28363708', '28363709', '28383947', '28383948', '28383949',
'28383950', '28383951', '28383952', '28383953', '28383954', '28383955',
'28383956', '28387068', '28387069', '28387070', '28387071', '28387072',
'28387073', '28387074', '28387075', '28389309', '28389310', '28389311',
'28389312', '28389313', '28389314', '28389315', '28389316', '28394980',
'28394981', '28394982', '28394983', '28394984', '28394985', '28394986',
'28394987', '28394988', '28394989', '28397842', '28397843', '28397844',
'28397845', '28397846', '28397847', '28397848', '28398182', '28398183',
'28398184', '28398185', '28398211', '28398212', '28398622', '28398623',
'28398624', '28398625', '28398626', '28398627', '28477648', '28477766',
'28477803', '28477813', '28477863', '28477932', '28477969', '28478048',
'28478049', '28478092', '28478129', '28478156', '28478157', '28478158',
'28478201', '28478202', '28478248', '28478312', '28478366', '28478410',
'28478412', '28478451', '28478479', '28478556', '28478672', '28478698',
'28478699', '28478751', '28478806', '28478822', '28479017', '28479018',
'28479019', '28479064', '28479075', '28479084', '28479117', '28479118',
'28479119', '28479120', '28496075', '28496076', '28496077', '28496078',
'28496079', '28496080', '28496081', '28496082', '28496083', '28496134',
'28496143', '28496144', '28496165', '28496175', '28496198', '28496199',
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'28521174', '28521175', '28521176', '28521177', '28521178', '28521179',
'28521180', '28521181', '28521182', '28521183', '28521184', '28521185',
'28521186', '28521187', '28521188', '28521189', '28521190', '28521191',
'28521192', '28521193', '28521194', '28521195', '28521196', '28521197',
'28521198', '28521199', '28521200', '28521202', '28521203', '28521204',
'28521205', '28521206', '28521207', '28521208', '28521209', '28521210',
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'28521222', '28521223', '28521224', '28521225', '28521226', '28521227',
'28521228', '28521229', '28521230', '28521231', '28521232', '28521233',
'28521234', '28521691', '28521692', '28521693', '28521694', '28521695',
'28521696', '28521697', '28521698', '28521699', '28521700', '28521705',
'28521706', '28521707', '28521708', '28521709', '28521710', '28521735',
'28521736', '28521737', '28521738', '28521741', '28521742', '28521743',
'28521744', '28521745', '28521746', '28521747', '28521748', '28521749',
'28521750', '28521751', '28521752', '28521753', '28521754', '28521755',
'28521756', '28521757', '28521758', '28521759', '28521760', '28521761',
'28521762', '28521763', '28521764', '28521765', '28521766', '28521767',
'28521768', '28521777', '28521778', '28521779', '28521780', '28521781',
'28521782', '28521783', '28521784', '28521785', '28521786', '28521787',
'28521788', '28521789', '28521790', '28521791', '28521792', '28521793',
'28521794', '28521795', '28521796', '28521797', '28521799', '28521800',
'28521801', '28521802', '28521803', '28521804', '28521805', '28521806',
'28521807', '28521808', '28521811', '28521812', '28521813', '28521814',
'28521815', '28521816', '28521817', '28521818', '28521819', '28521820',
'28521821', '28521822', '28521823', '28521824', '28521825', '28521826',
'28521829', '28521830', '28521831', '28521832', '28521833', '28521834',
'28521835', '28521836', '28521848', '28521849', '28521853', '28521854',
'28521855', '28521856', '28521857', '28521858', '28521859', '28521860',
'28521861', '28521862', '28521863', '28521864', '28521865', '28521866',
'28521867', '28521868', '28521869', '28521870', '28521871', '28521872',
'28521873', '28521874', '28521875', '28521876', '28521877', '28521907',
'28521908', '28521909', '28521910', '28521911', '28521912', '28521913',
'28521914', '28521915', '28521937', '28521938', '28521939', '28521940',
'28521941', '28521942', '28521943', '28521944', '28521945', '28521946',
'28521947', '28521948', '28521949', '28521950', '28521951', '28521952',
'28521953', '28521954', '28521955', '28521956', '28521957', '28521958',
'28521959', '28521960', '28521979', '28521980', '28521981', '28521982',
'28521983', '28521984', '28521985', '28521986', '28521987', '28521988',
'28521989', '28521990', '28521991', '28521992', '28521993', '28521994',
'28521995', '28521996', '28521997', '28521998', '28521999', '28522000',
'28522001', '28522002', '28522003', '28522004', '28522005', '28522006',
'28522007', '28522008', '28522009', '28522011', '28522012', '28522013',
'28522014', '28522015', '28522016', '28522017', '28522018', '28522019',
'28522020', '28522025', '28522026', '28522027', '28522028', '28522029',
'28522030', '28522031', '28522032', '28522033', '28522034', '28522035',
'28522036', '28522037', '28522038', '28522039', '28522040', '28522041',
'28522042', '28522043', '28522044', '28522045', '28522046', '28522047',
'28522048', '28522049', '28522050', '28522051', '28522052', '28522053',
'28522054', '28522055', '28522056', '28522057', '28522058', '28522059',
'28522060', '28522061', '28522062', '28522064', '28522065', '28522066',
'28522067', '28522068', '28522069', '28522070', '28522071', '28522072',
'28522073', '28522075', '28522076', '28522077', '28522078', '28522079',
'28522080', '28522081', '28522082', '28522083', '28522084', '28522087',
'28522088', '28522089', '28522090', '28522091', '28522092', '28522093',
'28522094', '28522095', '28522096', '28522097', '28522098', '28522099',
'28522100', '28522101', '28522102', '28522103', '28522104', '28522105',
'28522106', '28522118', '28522119', '28522120', '28522121', '28522122',
'28522123', '28522124', '28522125', '28522126', '28522127', '28578707',
'28579455', '28579456', '28579457', '28579458', '28579459', '28579460',
'28579487', '28579825', '28579826', '28580048', '28580049', '28580808',
'28580809', '28580810', '28580811', '28581369', '28581370', '28582537',
'28582538', '28582539', '28584020', '28584021', '28584022', '28584023',
'28584966', '28584967', '28584968', '28584969', '28588765', '28588766',
'28588767', '28589142', '28589143', '28589144', '28589659', '28589660',
'28589661', '28590510', '28593314', '28597880', '28597881', '28600467',
'28600495', '28600498', '28600499', '28600500', '28600501', '28600522',
'28600523', '28600539', '28600540', '28601205', '28601206', '28605809',
'28605810', '28609727', '28609728', '28609729', '28609730', '28962886',
'28962887', '28962888', '28962889', '28962890', '28962891', '28962892',
'28962893', '28962914', '28962915', '28964105', '28964106', '28964107',
'28964109', '28964128', '28964129', '28964150', '28964168', '28964169',
'28964170', '28964186', '28964187', '28964188', '28964189', '28964190',
'28964191', '28964200', '28964234', '28964235', '28964236', '28967071',
'28967072', '28967086', '28967087', '28967088', '28967106', '28967113',
'28967114', '28967115', '28967116', '28968285', '28968286', '28968287',
'28968288', '28968289', '28968290', '28968291', '28968292', '28968293',
'28968294', '28969249', '28969250', '28969251', '28969270', '28969271',
'28969272', '28969296', '28969297', '28969298', '28969299', '28972982',
'28972983', '28973000', '28973065', '28973066', '28973067', '28973068',
'28973078', '28973099', '28973100', '28976147', '28976148', '28976149',
'28976150', '28976151', '28976152', '28976153', '28976154', '28976155',
'28976202', '28977117', '28977143', '28977168', '28977177', '28977178',
'28977179', '28977218', '28977219', '28977220', '28977233', '28978143',
'28978169', '28978170', '28978171', '28978184', '28978212', '28978213',
'28978237', '28978238', '28978239', '28978824', '28978825', '28978826',
'28978841', '28978842', '28978850', '28978851', '28978852', '28978853',
'28978893', '28979237', '28979238', '28979239', '28979240', '28979251',
'28979290', '28979291', '28979292', '28979293', '28979331', '28982358',
'28982367', '28982368', '28982369', '28982370', '28982371', '28982372',
'28982373', '28982374', '28982375', '28984978', '28984979', '28984980',
'28984981', '28984982', '28984983', '28984984', '28985016', '28985017',
'28985052'}
-------------------------------------
-------------------------------------
count : 32

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1301, in optimizeGeometry
raise GeomOptNotConvergedError("Optimizer.optimizeGeometry() failed to converge.")
geometric.errors.GeomOptNotConvergedError: Optimizer.optimizeGeometry() failed to converge.


ids :
{'28394045', '28394046', '28394047', '28394048', '28394049', '28394343',
'28394344', '28394345', '28394346', '28394347', '28394869', '28394909',
'28394910', '28394911', '28394912', '28478411', '28478886', '28478903',
'28478937', '28478978', '28511180', '28511181', '28511182', '28511183',
'28511220', '28511221', '28511236', '28511237', '28511260', '28511261',
'28577239', '28577775'}
-------------------------------------
-------------------------------------
count : 1

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1299, in optimizeGeometry
self.evaluateStep()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1277, in evaluateStep
Eig1 = np.linalg.eigh(self.H)[0]
File "<__array_function__ internals>", line 6, in eigh
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 1471, in eigh
w, vt = gufunc(a, signature=signature, extobj=extobj)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 94, in _raise_linalgerror_eigenvalues_nonconvergence
raise LinAlgError("Eigenvalues did not converge")
numpy.linalg.LinAlgError: Eigenvalues did not converge


ids :
{'28816920'}
-------------------------------------
-------------------------------------
count : 1

Caught Executor Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.


ids :
{'28839719'}
-------------------------------------

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.222.g3eb3978
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

openff-dangerbot · 2020-10-28T12:41:41Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-10-28 12:41 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	ERROR
gfn2xtb	480	1	0
gfn1xtb	479	2	0
gfnff	295	30	156

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	32575	1	0
gfn1xtb	34197	3	0
gfnff	21351	96	901

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 868

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/programs/xtb.py", line 72, in compute
output = run_qcschema(input_data)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/xtb/qcschema/harness.py", line 208, in run_qcschema
return qcel.models.AtomicResult(**ret_data, stdout=output)
File "pydantic/main.py", line 346, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for AtomicResult
return_result
cannot reshape array of size 1 into shape (3) (type=value_error)



ids :
{'28348614', '28348615', '28348616', '28348617', '28348618', '28348619',
'28351111', '28351807', '28351834', '28351835', '28351836', '28351837',
'28351838', '28351839', '28351840', '28351841', '28351842', '28353283',
'28353284', '28353285', '28353286', '28353287', '28353288', '28355916',
'28355917', '28355918', '28355919', '28355920', '28355921', '28363700',
'28363701', '28363702', '28363703', '28363704', '28363705', '28363706',
'28363707', '28363708', '28363709', '28383947', '28383948', '28383949',
'28383950', '28383951', '28383952', '28383953', '28383954', '28383955',
'28383956', '28387068', '28387069', '28387070', '28387071', '28387072',
'28387073', '28387074', '28387075', '28389309', '28389310', '28389311',
'28389312', '28389313', '28389314', '28389315', '28389316', '28394980',
'28394981', '28394982', '28394983', '28394984', '28394985', '28394986',
'28394987', '28394988', '28394989', '28397842', '28397843', '28397844',
'28397845', '28397846', '28397847', '28397848', '28398182', '28398183',
'28398184', '28398185', '28398211', '28398212', '28398622', '28398623',
'28398624', '28398625', '28398626', '28398627', '28477648', '28477766',
'28477803', '28477813', '28477863', '28477932', '28477969', '28478048',
'28478049', '28478092', '28478129', '28478156', '28478157', '28478158',
'28478201', '28478202', '28478248', '28478312', '28478366', '28478410',
'28478412', '28478451', '28478479', '28478556', '28478672', '28478698',
'28478699', '28478751', '28478806', '28478822', '28479017', '28479018',
'28479019', '28479064', '28479075', '28479084', '28479117', '28479118',
'28479119', '28479120', '28496075', '28496076', '28496077', '28496078',
'28496079', '28496080', '28496081', '28496082', '28496083', '28496134',
'28496143', '28496144', '28496165', '28496175', '28496198', '28496199',
'28496200', '28496201', '28496202', '28510925', '28510926', '28510942',
'28510955', '28510974', '28510975', '28510976', '28510988', '28510989',
'28510990', '28510991', '28510992', '28510993', '28510994', '28510995',
'28510996', '28510997', '28510998', '28511025', '28511026', '28511030',
'28511031', '28511032', '28511039', '28511040', '28511041', '28511054',
'28511055', '28511056', '28511057', '28511058', '28511059', '28511071',
'28511072', '28511073', '28511074', '28511088', '28511103', '28511104',
'28511114', '28511137', '28511150', '28511161', '28511162', '28511163',
'28511164', '28511179', '28511308', '28511319', '28511331', '28511332',
'28511333', '28511334', '28511335', '28511336', '28511337', '28511338',
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'28521848', '28521849', '28521853', '28521854', '28521855', '28521856',
'28521857', '28521858', '28521859', '28521860', '28521861', '28521862',
'28521863', '28521864', '28521865', '28521866', '28521867', '28521868',
'28521869', '28521870', '28521871', '28521872', '28521873', '28521874',
'28521875', '28521876', '28521877', '28521907', '28521908', '28521909',
'28521910', '28521911', '28521912', '28521913', '28521914', '28521915',
'28521937', '28521938', '28521939', '28521940', '28521941', '28521942',
'28521943', '28521944', '28521945', '28521946', '28521947', '28521948',
'28521949', '28521950', '28521951', '28521952', '28521953', '28521954',
'28521955', '28521956', '28521957', '28521958', '28521959', '28521960',
'28521979', '28521980', '28521981', '28521982', '28521983', '28521984',
'28521985', '28521986', '28521987', '28521988', '28521989', '28521990',
'28521991', '28521992', '28521993', '28521994', '28521995', '28521996',
'28521997', '28521998', '28521999', '28522000', '28522001', '28522002',
'28522003', '28522004', '28522005', '28522006', '28522007', '28522008',
'28522009', '28522011', '28522012', '28522013', '28522014', '28522015',
'28522016', '28522017', '28522018', '28522019', '28522020', '28522025',
'28522026', '28522027', '28522028', '28522029', '28522030', '28522031',
'28522032', '28522033', '28522034', '28522035', '28522036', '28522037',
'28522038', '28522039', '28522040', '28522041', '28522042', '28522043',
'28522044', '28522045', '28522046', '28522047', '28522048', '28522049',
'28522050', '28522051', '28522052', '28522053', '28522054', '28522055',
'28522056', '28522057', '28522058', '28522059', '28522060', '28522061',
'28522062', '28522064', '28522065', '28522066', '28522067', '28522068',
'28522069', '28522070', '28522071', '28522072', '28522073', '28522075',
'28522076', '28522077', '28522078', '28522079', '28522080', '28522081',
'28522082', '28522083', '28522084', '28522087', '28522088', '28522089',
'28522090', '28522091', '28522092', '28522093', '28522094', '28522095',
'28522096', '28522097', '28522098', '28522099', '28522100', '28522101',
'28522102', '28522103', '28522104', '28522105', '28522106', '28522118',
'28522119', '28522120', '28522121', '28522122', '28522123', '28522124',
'28522125', '28522126', '28522127', '28578707', '28579455', '28579456',
'28579457', '28579458', '28579459', '28579460', '28579487', '28579825',
'28579826', '28580048', '28580049', '28580808', '28580809', '28580810',
'28580811', '28581369', '28581370', '28582537', '28582538', '28582539',
'28584020', '28584021', '28584022', '28584023', '28584966', '28584967',
'28584968', '28584969', '28588765', '28588766', '28588767', '28589142',
'28589143', '28589144', '28589659', '28589660', '28589661', '28590510',
'28593314', '28597880', '28597881', '28600467', '28600495', '28600498',
'28600499', '28600500', '28600501', '28600522', '28600523', '28600539',
'28600540', '28601205', '28601206', '28605809', '28605810', '28609727',
'28609728', '28609729', '28609730', '28962886', '28962887', '28962888',
'28962889', '28962890', '28962891', '28962892', '28962893', '28962914',
'28962915', '28964105', '28964106', '28964107', '28964109', '28964128',
'28964129', '28964150', '28964168', '28964169', '28964170', '28964186',
'28964187', '28964188', '28964189', '28964190', '28964191', '28964200',
'28964234', '28964235', '28964236', '28967071', '28967072', '28967086',
'28967087', '28967088', '28967106', '28967113', '28967114', '28967115',
'28967116', '28968285', '28968286', '28968287', '28968288', '28968289',
'28968290', '28968291', '28968292', '28968294', '28969249', '28969250',
'28969251', '28969270', '28969271', '28969272', '28969296', '28969297',
'28969298', '28969299', '28972982', '28972983', '28973000', '28973065',
'28973066', '28973067', '28973068', '28973078', '28973099', '28973100',
'28976147', '28976148', '28976149', '28976150', '28976151', '28976152',
'28976153', '28976154', '28976155', '28976202', '28977117', '28977143',
'28977168', '28977177', '28977178', '28977179', '28977218', '28977219',
'28977220', '28977233', '28978143', '28978169', '28978170', '28978171',
'28978184', '28978212', '28978213', '28978237', '28978238', '28978239',
'28978824', '28978825', '28978826', '28978841', '28978842', '28978850',
'28978851', '28978852', '28978853', '28978893', '28979237', '28979238',
'28979239', '28979240', '28979251', '28979290', '28979291', '28979292',
'28979293', '28979331', '28982358', '28982367', '28982368', '28982369',
'28982370', '28982371', '28982372', '28982373', '28982374', '28982375',
'28984978', '28984979', '28984980', '28984981', '28984982', '28984983',
'28984984', '28985016', '28985017', '28985052'}
-------------------------------------
-------------------------------------
count : 32

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1301, in optimizeGeometry
raise GeomOptNotConvergedError("Optimizer.optimizeGeometry() failed to converge.")
geometric.errors.GeomOptNotConvergedError: Optimizer.optimizeGeometry() failed to converge.


ids :
{'28394045', '28394046', '28394047', '28394048', '28394049', '28394343',
'28394344', '28394345', '28394346', '28394347', '28394869', '28394909',
'28394910', '28394911', '28394912', '28478411', '28478886', '28478903',
'28478937', '28478978', '28511180', '28511181', '28511182', '28511183',
'28511220', '28511221', '28511236', '28511237', '28511260', '28511261',
'28577239', '28577775'}
-------------------------------------
-------------------------------------
count : 1

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1299, in optimizeGeometry
self.evaluateStep()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1277, in evaluateStep
Eig1 = np.linalg.eigh(self.H)[0]
File "<__array_function__ internals>", line 6, in eigh
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 1471, in eigh
w, vt = gufunc(a, signature=signature, extobj=extobj)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 94, in _raise_linalgerror_eigenvalues_nonconvergence
raise LinAlgError("Eigenvalues did not converge")
numpy.linalg.LinAlgError: Eigenvalues did not converge


ids :
{'28816920'}
-------------------------------------

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.222.g3eb3978
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

openff-dangerbot · 2020-10-29T12:41:57Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-10-29 12:41 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	ERROR
gfn2xtb	480	1	0
gfn1xtb	480	1	0
gfnff	317	8	156

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	32575	1	0
gfn1xtb	34205	1	0
gfnff	21835	9	904

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 871

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/programs/xtb.py", line 72, in compute
output = run_qcschema(input_data)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/xtb/qcschema/harness.py", line 208, in run_qcschema
return qcel.models.AtomicResult(**ret_data, stdout=output)
File "pydantic/main.py", line 346, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for AtomicResult
return_result
cannot reshape array of size 1 into shape (3) (type=value_error)



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'28511623', '28511624', '28511625', '28520161', '28520202', '28520235',
'28520236', '28520267', '28520268', '28520269', '28520270', '28520271',
'28520272', '28520273', '28520274', '28520275', '28520305', '28520306',
'28520307', '28520308', '28520309', '28520344', '28520348', '28520415',
'28520607', '28520638', '28520669', '28520670', '28520695', '28520705',
'28520737', '28520738', '28520743', '28520771', '28520772', '28520773',
'28520774', '28520775', '28520798', '28520812', '28520813', '28520814',
'28521103', '28521104', '28521105', '28521106', '28521107', '28521108',
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'28521198', '28521199', '28521200', '28521202', '28521203', '28521204',
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'28521908', '28521909', '28521910', '28521911', '28521912', '28521913',
'28521914', '28521915', '28521937', '28521938', '28521939', '28521940',
'28521941', '28521942', '28521943', '28521944', '28521945', '28521946',
'28521947', '28521948', '28521949', '28521950', '28521951', '28521952',
'28521953', '28521954', '28521955', '28521956', '28521957', '28521958',
'28521959', '28521960', '28521979', '28521980', '28521981', '28521982',
'28521983', '28521984', '28521985', '28521986', '28521987', '28521988',
'28521989', '28521990', '28521991', '28521992', '28521993', '28521994',
'28521995', '28521996', '28521997', '28521998', '28521999', '28522000',
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'28522014', '28522015', '28522016', '28522017', '28522018', '28522019',
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'28522060', '28522061', '28522062', '28522064', '28522065', '28522066',
'28522067', '28522068', '28522069', '28522070', '28522071', '28522072',
'28522073', '28522075', '28522076', '28522077', '28522078', '28522079',
'28522080', '28522081', '28522082', '28522083', '28522084', '28522087',
'28522088', '28522089', '28522090', '28522091', '28522092', '28522093',
'28522094', '28522095', '28522096', '28522097', '28522098', '28522099',
'28522100', '28522101', '28522102', '28522103', '28522104', '28522105',
'28522106', '28522118', '28522119', '28522120', '28522121', '28522122',
'28522123', '28522124', '28522125', '28522126', '28522127', '28578707',
'28579455', '28579456', '28579457', '28579458', '28579459', '28579460',
'28579487', '28579825', '28579826', '28580048', '28580049', '28580808',
'28580809', '28580810', '28580811', '28581369', '28581370', '28582537',
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'28584966', '28584967', '28584968', '28584969', '28588765', '28588766',
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'28967114', '28967115', '28967116', '28968285', '28968286', '28968287',
'28968288', '28968289', '28968290', '28968291', '28968292', '28968293',
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'28972983', '28973000', '28973065', '28973066', '28973067', '28973068',
'28973078', '28973099', '28973100', '28976147', '28976148', '28976149',
'28976150', '28976151', '28976152', '28976153', '28976154', '28976155',
'28976202', '28977117', '28977143', '28977168', '28977177', '28977178',
'28977179', '28977218', '28977219', '28977220', '28977233', '28978143',
'28978169', '28978170', '28978171', '28978184', '28978212', '28978213',
'28978237', '28978238', '28978239', '28978824', '28978825', '28978826',
'28978841', '28978842', '28978850', '28978851', '28978852', '28978853',
'28978893', '28979237', '28979238', '28979239', '28979240', '28979251',
'28979290', '28979291', '28979292', '28979293', '28979331', '28982358',
'28982367', '28982368', '28982369', '28982370', '28982371', '28982372',
'28982373', '28982374', '28982375', '28984978', '28984979', '28984980',
'28984981', '28984982', '28984983', '28984984', '28985016', '28985017',
'28985052'}
-------------------------------------
-------------------------------------
count : 32

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1301, in optimizeGeometry
raise GeomOptNotConvergedError("Optimizer.optimizeGeometry() failed to converge.")
geometric.errors.GeomOptNotConvergedError: Optimizer.optimizeGeometry() failed to converge.


ids :
{'28394045', '28394046', '28394047', '28394048', '28394049', '28394343',
'28394344', '28394345', '28394346', '28394347', '28394869', '28394909',
'28394910', '28394911', '28394912', '28478411', '28478886', '28478903',
'28478937', '28478978', '28511180', '28511181', '28511182', '28511183',
'28511220', '28511221', '28511236', '28511237', '28511260', '28511261',
'28577239', '28577775'}
-------------------------------------
-------------------------------------
count : 1

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1299, in optimizeGeometry
self.evaluateStep()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1277, in evaluateStep
Eig1 = np.linalg.eigh(self.H)[0]
File "<__array_function__ internals>", line 6, in eigh
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 1471, in eigh
w, vt = gufunc(a, signature=signature, extobj=extobj)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 94, in _raise_linalgerror_eigenvalues_nonconvergence
raise LinAlgError("Eigenvalues did not converge")
numpy.linalg.LinAlgError: Eigenvalues did not converge


ids :
{'28816920'}
-------------------------------------

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.222.g3eb3978
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

openff-dangerbot · 2020-10-30T12:27:27Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-10-30 12:27 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	ERROR
gfn2xtb	480	1	0
gfn1xtb	480	1	0
gfnff	320	5	156

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	32575	1	0
gfn1xtb	34205	1	0
gfnff	21887	14	903

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 870

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/programs/xtb.py", line 72, in compute
output = run_qcschema(input_data)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/xtb/qcschema/harness.py", line 208, in run_qcschema
return qcel.models.AtomicResult(**ret_data, stdout=output)
File "pydantic/main.py", line 346, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for AtomicResult
return_result
cannot reshape array of size 1 into shape (3) (type=value_error)



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'28521873', '28521874', '28521875', '28521876', '28521877', '28521907',
'28521908', '28521909', '28521910', '28521911', '28521912', '28521913',
'28521914', '28521915', '28521937', '28521938', '28521939', '28521940',
'28521941', '28521942', '28521943', '28521944', '28521945', '28521946',
'28521947', '28521948', '28521949', '28521950', '28521951', '28521952',
'28521953', '28521954', '28521955', '28521956', '28521957', '28521958',
'28521959', '28521960', '28521979', '28521980', '28521981', '28521982',
'28521983', '28521984', '28521985', '28521986', '28521987', '28521988',
'28521989', '28521990', '28521991', '28521992', '28521993', '28521994',
'28521995', '28521996', '28521997', '28521998', '28521999', '28522000',
'28522001', '28522002', '28522003', '28522004', '28522005', '28522006',
'28522007', '28522008', '28522009', '28522011', '28522012', '28522013',
'28522014', '28522015', '28522016', '28522017', '28522018', '28522019',
'28522020', '28522025', '28522026', '28522027', '28522028', '28522029',
'28522030', '28522031', '28522032', '28522033', '28522034', '28522035',
'28522036', '28522037', '28522038', '28522039', '28522040', '28522041',
'28522042', '28522043', '28522044', '28522045', '28522046', '28522047',
'28522048', '28522049', '28522050', '28522051', '28522052', '28522053',
'28522054', '28522055', '28522056', '28522057', '28522058', '28522059',
'28522060', '28522061', '28522062', '28522064', '28522065', '28522066',
'28522067', '28522068', '28522069', '28522070', '28522071', '28522072',
'28522073', '28522075', '28522076', '28522077', '28522078', '28522079',
'28522080', '28522081', '28522082', '28522083', '28522084', '28522087',
'28522088', '28522089', '28522090', '28522091', '28522092', '28522093',
'28522094', '28522095', '28522096', '28522097', '28522098', '28522100',
'28522101', '28522102', '28522103', '28522104', '28522105', '28522106',
'28522118', '28522119', '28522120', '28522121', '28522122', '28522123',
'28522124', '28522125', '28522126', '28522127', '28578707', '28579455',
'28579456', '28579457', '28579458', '28579459', '28579460', '28579487',
'28579825', '28579826', '28580048', '28580049', '28580808', '28580809',
'28580810', '28580811', '28581369', '28581370', '28582537', '28582538',
'28582539', '28584020', '28584021', '28584022', '28584023', '28584966',
'28584967', '28584968', '28584969', '28588765', '28588766', '28588767',
'28589142', '28589143', '28589144', '28589659', '28589660', '28589661',
'28590510', '28593314', '28597880', '28597881', '28600467', '28600495',
'28600498', '28600499', '28600500', '28600501', '28600522', '28600523',
'28600539', '28600540', '28601205', '28601206', '28605809', '28605810',
'28609727', '28609728', '28609729', '28609730', '28962886', '28962887',
'28962888', '28962889', '28962890', '28962891', '28962892', '28962893',
'28962914', '28962915', '28964105', '28964106', '28964107', '28964109',
'28964128', '28964129', '28964150', '28964168', '28964169', '28964170',
'28964186', '28964187', '28964188', '28964189', '28964190', '28964191',
'28964200', '28964234', '28964235', '28964236', '28967071', '28967072',
'28967086', '28967087', '28967088', '28967106', '28967113', '28967114',
'28967115', '28967116', '28968285', '28968286', '28968287', '28968288',
'28968289', '28968290', '28968291', '28968292', '28968293', '28968294',
'28969249', '28969250', '28969251', '28969270', '28969271', '28969272',
'28969296', '28969297', '28969298', '28969299', '28972982', '28972983',
'28973000', '28973065', '28973066', '28973067', '28973068', '28973078',
'28973099', '28973100', '28976147', '28976148', '28976149', '28976150',
'28976151', '28976152', '28976153', '28976154', '28976155', '28976202',
'28977117', '28977143', '28977168', '28977177', '28977178', '28977179',
'28977218', '28977219', '28977220', '28977233', '28978143', '28978169',
'28978170', '28978171', '28978184', '28978212', '28978213', '28978237',
'28978238', '28978239', '28978824', '28978825', '28978826', '28978841',
'28978842', '28978850', '28978851', '28978852', '28978853', '28978893',
'28979237', '28979238', '28979239', '28979240', '28979251', '28979290',
'28979291', '28979292', '28979293', '28979331', '28982358', '28982367',
'28982368', '28982369', '28982370', '28982371', '28982372', '28982373',
'28982374', '28982375', '28984978', '28984979', '28984980', '28984981',
'28984982', '28984983', '28984984', '28985016', '28985017', '28985052'}
-------------------------------------
-------------------------------------
count : 32

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1301, in optimizeGeometry
raise GeomOptNotConvergedError("Optimizer.optimizeGeometry() failed to converge.")
geometric.errors.GeomOptNotConvergedError: Optimizer.optimizeGeometry() failed to converge.


ids :
{'28394045', '28394046', '28394047', '28394048', '28394049', '28394343',
'28394344', '28394345', '28394346', '28394347', '28394869', '28394909',
'28394910', '28394911', '28394912', '28478411', '28478886', '28478903',
'28478937', '28478978', '28511180', '28511181', '28511182', '28511183',
'28511220', '28511221', '28511236', '28511237', '28511260', '28511261',
'28577239', '28577775'}
-------------------------------------
-------------------------------------
count : 1

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1299, in optimizeGeometry
self.evaluateStep()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1277, in evaluateStep
Eig1 = np.linalg.eigh(self.H)[0]
File "<__array_function__ internals>", line 6, in eigh
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 1471, in eigh
w, vt = gufunc(a, signature=signature, extobj=extobj)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 94, in _raise_linalgerror_eigenvalues_nonconvergence
raise LinAlgError("Eigenvalues did not converge")
numpy.linalg.LinAlgError: Eigenvalues did not converge


ids :
{'28816920'}
-------------------------------------

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.222.g3eb3978
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

openff-dangerbot · 2020-10-31T12:25:59Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-10-31 12:25 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING
gfn2xtb	480	1
gfn1xtb	480	1
gfnff	320	161

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
gfn2xtb	32575	1
gfn1xtb	34205	1
gfnff	21887	917

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.222.g3eb3978
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

openff-dangerbot · 2020-11-01T12:26:15Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-11-01 12:26 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING
gfn2xtb	480	1
gfn1xtb	480	1
gfnff	320	161

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
gfn2xtb	32575	1
gfn1xtb	34205	1
gfnff	21887	917

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.222.g3eb3978
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

openff-dangerbot · 2020-11-02T12:28:57Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-11-02 12:28 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING
gfn2xtb	480	1
gfn1xtb	480	1
gfnff	320	161

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
gfn2xtb	32575	1
gfn1xtb	34205	1
gfnff	21887	917

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.222.g3eb3978
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

openff-dangerbot · 2020-11-03T12:31:47Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-11-03 12:31 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	ERROR
gfn2xtb	480	1	0
gfn1xtb	480	1	0
gfnff	321	4	156

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	32575	1	0
gfn1xtb	34205	1	0
gfnff	21899	32	901

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 868

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/programs/xtb.py", line 72, in compute
output = run_qcschema(input_data)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/xtb/qcschema/harness.py", line 208, in run_qcschema
return qcel.models.AtomicResult(**ret_data, stdout=output)
File "pydantic/main.py", line 346, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for AtomicResult
return_result
cannot reshape array of size 1 into shape (3) (type=value_error)



ids :
{'28348615', '28348616', '28348617', '28348618', '28348619', '28351111',
'28351807', '28351834', '28351835', '28351836', '28351837', '28351838',
'28351839', '28351840', '28351841', '28351842', '28353283', '28353284',
'28353285', '28353286', '28353287', '28353288', '28355916', '28355917',
'28355918', '28355919', '28355920', '28355921', '28363700', '28363701',
'28363702', '28363703', '28363704', '28363705', '28363706', '28363707',
'28363708', '28363709', '28383947', '28383948', '28383949', '28383950',
'28383951', '28383952', '28383953', '28383954', '28383955', '28383956',
'28387068', '28387069', '28387070', '28387071', '28387072', '28387073',
'28387074', '28387075', '28389309', '28389310', '28389311', '28389312',
'28389313', '28389314', '28389315', '28389316', '28394980', '28394981',
'28394982', '28394983', '28394984', '28394985', '28394986', '28394987',
'28394988', '28394989', '28397842', '28397843', '28397844', '28397845',
'28397846', '28397847', '28397848', '28398182', '28398183', '28398184',
'28398185', '28398211', '28398212', '28398622', '28398623', '28398624',
'28398625', '28398626', '28398627', '28477648', '28477766', '28477803',
'28477813', '28477863', '28477932', '28477969', '28478048', '28478049',
'28478092', '28478129', '28478156', '28478157', '28478158', '28478201',
'28478202', '28478248', '28478312', '28478366', '28478410', '28478412',
'28478451', '28478479', '28478556', '28478672', '28478698', '28478699',
'28478751', '28478806', '28478822', '28479017', '28479018', '28479019',
'28479064', '28479075', '28479084', '28479117', '28479118', '28479119',
'28479120', '28496075', '28496076', '28496077', '28496078', '28496079',
'28496080', '28496081', '28496082', '28496083', '28496144', '28496165',
'28496175', '28496198', '28496199', '28496200', '28496201', '28496202',
'28510925', '28510926', '28510942', '28510955', '28510974', '28510975',
'28510976', '28510988', '28510989', '28510990', '28510991', '28510992',
'28510993', '28510994', '28510995', '28510996', '28510997', '28510998',
'28511025', '28511026', '28511030', '28511031', '28511032', '28511039',
'28511040', '28511041', '28511054', '28511055', '28511056', '28511057',
'28511058', '28511059', '28511071', '28511072', '28511073', '28511074',
'28511088', '28511103', '28511104', '28511114', '28511137', '28511150',
'28511161', '28511162', '28511163', '28511164', '28511179', '28511308',
'28511319', '28511331', '28511332', '28511333', '28511334', '28511335',
'28511336', '28511337', '28511338', '28511390', '28511391', '28511392',
'28511393', '28511407', '28511416', '28511417', '28511418', '28511419',
'28511420', '28511433', '28511434', '28511435', '28511451', '28511457',
'28511458', '28511459', '28511460', '28511461', '28511462', '28511463',
'28511464', '28511465', '28511466', '28511467', '28511494', '28511557',
'28511559', '28511593', '28511594', '28511595', '28511596', '28511605',
'28511614', '28511615', '28511616', '28511617', '28511618', '28511619',
'28511620', '28511621', '28511622', '28511623', '28511624', '28511625',
'28520161', '28520202', '28520235', '28520236', '28520267', '28520268',
'28520269', '28520270', '28520271', '28520272', '28520273', '28520274',
'28520275', '28520305', '28520306', '28520307', '28520308', '28520309',
'28520344', '28520348', '28520415', '28520607', '28520638', '28520669',
'28520670', '28520695', '28520705', '28520737', '28520738', '28520743',
'28520771', '28520772', '28520773', '28520774', '28520775', '28520798',
'28520812', '28520813', '28520814', '28521103', '28521104', '28521105',
'28521106', '28521107', '28521108', '28521109', '28521110', '28521111',
'28521112', '28521143', '28521144', '28521145', '28521146', '28521147',
'28521148', '28521149', '28521150', '28521151', '28521152', '28521155',
'28521165', '28521166', '28521167', '28521168', '28521169', '28521170',
'28521171', '28521172', '28521173', '28521174', '28521175', '28521176',
'28521177', '28521178', '28521179', '28521180', '28521181', '28521182',
'28521183', '28521184', '28521185', '28521186', '28521187', '28521188',
'28521189', '28521190', '28521191', '28521192', '28521193', '28521194',
'28521195', '28521196', '28521197', '28521198', '28521199', '28521200',
'28521202', '28521203', '28521204', '28521205', '28521206', '28521207',
'28521208', '28521209', '28521210', '28521211', '28521217', '28521218',
'28521219', '28521220', '28521221', '28521222', '28521223', '28521224',
'28521225', '28521226', '28521227', '28521228', '28521229', '28521230',
'28521231', '28521232', '28521233', '28521234', '28521691', '28521692',
'28521693', '28521694', '28521695', '28521696', '28521697', '28521698',
'28521699', '28521700', '28521705', '28521706', '28521707', '28521708',
'28521709', '28521710', '28521735', '28521736', '28521737', '28521738',
'28521741', '28521742', '28521743', '28521744', '28521745', '28521746',
'28521747', '28521748', '28521749', '28521750', '28521751', '28521752',
'28521753', '28521754', '28521755', '28521756', '28521757', '28521758',
'28521759', '28521760', '28521761', '28521762', '28521763', '28521764',
'28521765', '28521766', '28521767', '28521768', '28521777', '28521778',
'28521779', '28521780', '28521781', '28521782', '28521783', '28521784',
'28521785', '28521786', '28521787', '28521788', '28521789', '28521790',
'28521791', '28521792', '28521793', '28521794', '28521795', '28521796',
'28521797', '28521799', '28521800', '28521801', '28521802', '28521803',
'28521804', '28521805', '28521806', '28521807', '28521808', '28521811',
'28521812', '28521813', '28521814', '28521815', '28521816', '28521817',
'28521818', '28521819', '28521820', '28521821', '28521822', '28521823',
'28521824', '28521825', '28521826', '28521829', '28521830', '28521831',
'28521832', '28521833', '28521834', '28521835', '28521836', '28521848',
'28521849', '28521853', '28521854', '28521855', '28521856', '28521857',
'28521858', '28521859', '28521860', '28521861', '28521862', '28521863',
'28521864', '28521865', '28521866', '28521867', '28521868', '28521869',
'28521870', '28521871', '28521872', '28521873', '28521874', '28521875',
'28521876', '28521877', '28521907', '28521908', '28521909', '28521910',
'28521911', '28521912', '28521913', '28521914', '28521915', '28521937',
'28521938', '28521939', '28521940', '28521941', '28521942', '28521943',
'28521944', '28521945', '28521946', '28521947', '28521948', '28521949',
'28521950', '28521951', '28521952', '28521953', '28521954', '28521955',
'28521956', '28521957', '28521958', '28521959', '28521960', '28521979',
'28521980', '28521981', '28521982', '28521983', '28521984', '28521985',
'28521986', '28521987', '28521988', '28521989', '28521990', '28521991',
'28521992', '28521993', '28521994', '28521995', '28521996', '28521997',
'28521998', '28521999', '28522000', '28522001', '28522002', '28522003',
'28522004', '28522005', '28522006', '28522007', '28522008', '28522009',
'28522011', '28522012', '28522013', '28522014', '28522015', '28522016',
'28522017', '28522018', '28522019', '28522020', '28522025', '28522026',
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'28522033', '28522034', '28522035', '28522036', '28522037', '28522038',
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'28522057', '28522058', '28522059', '28522060', '28522061', '28522062',
'28522064', '28522065', '28522066', '28522067', '28522068', '28522069',
'28522070', '28522071', '28522072', '28522073', '28522075', '28522076',
'28522077', '28522078', '28522079', '28522080', '28522081', '28522082',
'28522083', '28522084', '28522087', '28522088', '28522089', '28522090',
'28522091', '28522092', '28522093', '28522094', '28522095', '28522096',
'28522097', '28522098', '28522099', '28522100', '28522101', '28522102',
'28522103', '28522104', '28522105', '28522106', '28522118', '28522119',
'28522120', '28522121', '28522122', '28522123', '28522124', '28522125',
'28522126', '28522127', '28578707', '28579455', '28579456', '28579457',
'28579458', '28579459', '28579460', '28579487', '28579825', '28579826',
'28580048', '28580049', '28580808', '28580809', '28580810', '28580811',
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'28584021', '28584022', '28584023', '28584966', '28584967', '28584968',
'28584969', '28588765', '28588766', '28588767', '28589142', '28589143',
'28589144', '28589659', '28589660', '28589661', '28590510', '28593314',
'28597880', '28597881', '28600467', '28600495', '28600498', '28600499',
'28600500', '28600501', '28600522', '28600523', '28600539', '28600540',
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'28968285', '28968286', '28968287', '28968288', '28968289', '28968290',
'28968291', '28968292', '28968293', '28968294', '28969249', '28969250',
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'28969298', '28969299', '28972982', '28972983', '28973000', '28973065',
'28973066', '28973067', '28973068', '28973078', '28973099', '28973100',
'28976147', '28976148', '28976149', '28976150', '28976151', '28976152',
'28976153', '28976154', '28976155', '28976202', '28977117', '28977143',
'28977168', '28977177', '28977178', '28977179', '28977218', '28977219',
'28977220', '28977233', '28978143', '28978169', '28978170', '28978171',
'28978184', '28978212', '28978213', '28978237', '28978238', '28978239',
'28978824', '28978825', '28978826', '28978841', '28978842', '28978850',
'28978851', '28978852', '28978853', '28978893', '28979237', '28979238',
'28979239', '28979240', '28979251', '28979290', '28979291', '28979292',
'28979293', '28979331', '28982358', '28982367', '28982368', '28982369',
'28982370', '28982371', '28982372', '28982373', '28982374', '28982375',
'28984978', '28984979', '28984980', '28984981', '28984982', '28984983',
'28984984', '28985016', '28985017', '28985052'}
-------------------------------------
-------------------------------------
count : 32

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1301, in optimizeGeometry
raise GeomOptNotConvergedError("Optimizer.optimizeGeometry() failed to converge.")
geometric.errors.GeomOptNotConvergedError: Optimizer.optimizeGeometry() failed to converge.


ids :
{'28394045', '28394046', '28394047', '28394048', '28394049', '28394343',
'28394344', '28394345', '28394346', '28394347', '28394869', '28394909',
'28394910', '28394911', '28394912', '28478411', '28478886', '28478903',
'28478937', '28478978', '28511180', '28511181', '28511182', '28511183',
'28511220', '28511221', '28511236', '28511237', '28511260', '28511261',
'28577239', '28577775'}
-------------------------------------
-------------------------------------
count : 1

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1299, in optimizeGeometry
self.evaluateStep()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1277, in evaluateStep
Eig1 = np.linalg.eigh(self.H)[0]
File "<__array_function__ internals>", line 6, in eigh
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 1471, in eigh
w, vt = gufunc(a, signature=signature, extobj=extobj)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 94, in _raise_linalgerror_eigenvalues_nonconvergence
raise LinAlgError("Eigenvalues did not converge")
numpy.linalg.LinAlgError: Eigenvalues did not converge


ids :
{'28816920'}
-------------------------------------

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.222.g3eb3978
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

openff-dangerbot · 2020-11-04T12:37:08Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-11-04 12:37 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	ERROR
gfn2xtb	480	1	0
gfn1xtb	480	1	0
gfnff	321	4	156

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	32575	1	0
gfn1xtb	34205	1	0
gfnff	21927	24	901

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 868

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/programs/xtb.py", line 72, in compute
output = run_qcschema(input_data)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/xtb/qcschema/harness.py", line 208, in run_qcschema
return qcel.models.AtomicResult(**ret_data, stdout=output)
File "pydantic/main.py", line 346, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for AtomicResult
return_result
cannot reshape array of size 1 into shape (3) (type=value_error)



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'28579458', '28579459', '28579460', '28579487', '28579825', '28579826',
'28580048', '28580049', '28580808', '28580809', '28580810', '28580811',
'28581369', '28581370', '28582537', '28582538', '28582539', '28584020',
'28584021', '28584022', '28584023', '28584966', '28584967', '28584968',
'28584969', '28588765', '28588766', '28588767', '28589142', '28589143',
'28589144', '28589659', '28589660', '28589661', '28590510', '28593314',
'28597880', '28597881', '28600467', '28600495', '28600498', '28600499',
'28600500', '28600501', '28600522', '28600523', '28600539', '28600540',
'28601205', '28601206', '28605809', '28605810', '28609727', '28609728',
'28609729', '28609730', '28962886', '28962887', '28962888', '28962889',
'28962890', '28962891', '28962892', '28962893', '28962914', '28962915',
'28964105', '28964106', '28964107', '28964109', '28964128', '28964129',
'28964150', '28964168', '28964169', '28964170', '28964186', '28964187',
'28964188', '28964189', '28964190', '28964191', '28964200', '28964234',
'28964235', '28964236', '28967071', '28967072', '28967086', '28967087',
'28967088', '28967106', '28967113', '28967114', '28967115', '28967116',
'28968285', '28968286', '28968287', '28968288', '28968289', '28968290',
'28968291', '28968292', '28968293', '28968294', '28969249', '28969250',
'28969251', '28969270', '28969271', '28969272', '28969296', '28969297',
'28969298', '28969299', '28972982', '28972983', '28973000', '28973065',
'28973066', '28973067', '28973068', '28973078', '28973099', '28973100',
'28976147', '28976148', '28976149', '28976150', '28976151', '28976152',
'28976153', '28976154', '28976155', '28976202', '28977117', '28977143',
'28977168', '28977177', '28977178', '28977179', '28977218', '28977219',
'28977220', '28977233', '28978143', '28978169', '28978170', '28978171',
'28978184', '28978212', '28978213', '28978237', '28978238', '28978239',
'28978824', '28978825', '28978826', '28978841', '28978842', '28978850',
'28978851', '28978852', '28978853', '28978893', '28979237', '28979238',
'28979239', '28979240', '28979251', '28979290', '28979291', '28979292',
'28979293', '28979331', '28982358', '28982367', '28982368', '28982369',
'28982370', '28982371', '28982372', '28982373', '28982374', '28982375',
'28984978', '28984979', '28984980', '28984981', '28984982', '28984983',
'28984984', '28985016', '28985017', '28985052'}
-------------------------------------
-------------------------------------
count : 32

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1301, in optimizeGeometry
raise GeomOptNotConvergedError("Optimizer.optimizeGeometry() failed to converge.")
geometric.errors.GeomOptNotConvergedError: Optimizer.optimizeGeometry() failed to converge.


ids :
{'28394045', '28394046', '28394047', '28394048', '28394049', '28394343',
'28394344', '28394345', '28394346', '28394347', '28394869', '28394909',
'28394910', '28394911', '28394912', '28478411', '28478886', '28478903',
'28478937', '28478978', '28511180', '28511181', '28511182', '28511183',
'28511220', '28511221', '28511236', '28511237', '28511260', '28511261',
'28577239', '28577775'}
-------------------------------------
-------------------------------------
count : 1

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1299, in optimizeGeometry
self.evaluateStep()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1277, in evaluateStep
Eig1 = np.linalg.eigh(self.H)[0]
File "<__array_function__ internals>", line 6, in eigh
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 1471, in eigh
w, vt = gufunc(a, signature=signature, extobj=extobj)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 94, in _raise_linalgerror_eigenvalues_nonconvergence
raise LinAlgError("Eigenvalues did not converge")
numpy.linalg.LinAlgError: Eigenvalues did not converge


ids :
{'28816920'}
-------------------------------------

QCSubmit version information(click to expand)

	version
qcsubmit	0+untagged.222.g3eb3978
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

openff-dangerbot · 2020-11-05T12:37:01Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-11-05 12:37 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	ERROR
gfn2xtb	480	1	0
gfn1xtb	480	1	0
gfnff	321	4	156

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	32575	1	0
gfn1xtb	34205	1	0
gfnff	21927	27	898

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 866

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/programs/xtb.py", line 72, in compute
output = run_qcschema(input_data)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/xtb/qcschema/harness.py", line 208, in run_qcschema
return qcel.models.AtomicResult(**ret_data, stdout=output)
File "pydantic/main.py", line 346, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for AtomicResult
return_result
cannot reshape array of size 1 into shape (3) (type=value_error)



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'28978826', '28978841', '28978842', '28978850', '28978851', '28978852',
'28978853', '28978893', '28979237', '28979238', '28979239', '28979240',
'28979251', '28979290', '28979291', '28979292', '28979293', '28979331',
'28982358', '28982367', '28982368', '28982369', '28982370', '28982371',
'28982372', '28982373', '28982374', '28982375', '28984978', '28984979',
'28984980', '28984981', '28984982', '28984983', '28984984', '28985016',
'28985017', '28985052'}
-------------------------------------
-------------------------------------
count : 30

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1301, in optimizeGeometry
raise GeomOptNotConvergedError("Optimizer.optimizeGeometry() failed to converge.")
geometric.errors.GeomOptNotConvergedError: Optimizer.optimizeGeometry() failed to converge.


ids :
{'28394045', '28394046', '28394047', '28394049', '28394343', '28394344',
'28394345', '28394346', '28394347', '28394869', '28394909', '28394910',
'28394912', '28478411', '28478886', '28478903', '28478937', '28478978',
'28511180', '28511181', '28511182', '28511183', '28511220', '28511221',
'28511236', '28511237', '28511260', '28511261', '28577239', '28577775'}
-------------------------------------
-------------------------------------
count : 1

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1299, in optimizeGeometry
self.evaluateStep()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1277, in evaluateStep
Eig1 = np.linalg.eigh(self.H)[0]
File "<__array_function__ internals>", line 6, in eigh
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 1471, in eigh
w, vt = gufunc(a, signature=signature, extobj=extobj)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 94, in _raise_linalgerror_eigenvalues_nonconvergence
raise LinAlgError("Eigenvalues did not converge")
numpy.linalg.LinAlgError: Eigenvalues did not converge


ids :
{'28816920'}
-------------------------------------
-------------------------------------
count : 1

Caught Executor Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.


ids :
{'28394911'}
-------------------------------------

QCSubmit version information(click to expand)

	version
qcsubmit	v0.1.0
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

openff-dangerbot · 2020-11-06T12:33:17Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-11-06 12:33 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	ERROR
gfn2xtb	480	1	0
gfn1xtb	480	1	0
gfnff	321	4	156

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	32575	1	0
gfn1xtb	34205	1	0
gfnff	21927	29	896

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 861

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/programs/xtb.py", line 72, in compute
output = run_qcschema(input_data)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/xtb/qcschema/harness.py", line 208, in run_qcschema
return qcel.models.AtomicResult(**ret_data, stdout=output)
File "pydantic/main.py", line 346, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for AtomicResult
return_result
cannot reshape array of size 1 into shape (3) (type=value_error)



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'28968292', '28968293', '28968294', '28969249', '28969250', '28969251',
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'28978212', '28978213', '28978237', '28978238', '28978239', '28978824',
'28978825', '28978826', '28978841', '28978842', '28978850', '28978851',
'28978852', '28978853', '28978893', '28979237', '28979238', '28979239',
'28979240', '28979251', '28979290', '28979291', '28979292', '28979293',
'28979331', '28982358', '28982367', '28982368', '28982369', '28982370',
'28982371', '28982372', '28982373', '28982374', '28982375', '28984978',
'28984979', '28984980', '28984981', '28984982', '28984983', '28984984',
'28985016', '28985017', '28985052'}
-------------------------------------
-------------------------------------
count : 32

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1301, in optimizeGeometry
raise GeomOptNotConvergedError("Optimizer.optimizeGeometry() failed to converge.")
geometric.errors.GeomOptNotConvergedError: Optimizer.optimizeGeometry() failed to converge.


ids :
{'28394045', '28394046', '28394047', '28394048', '28394049', '28394343',
'28394344', '28394345', '28394346', '28394347', '28394869', '28394909',
'28394910', '28394911', '28394912', '28478411', '28478886', '28478903',
'28478937', '28478978', '28511180', '28511181', '28511182', '28511183',
'28511220', '28511221', '28511236', '28511237', '28511260', '28511261',
'28577239', '28577775'}
-------------------------------------
-------------------------------------
count : 1

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1299, in optimizeGeometry
self.evaluateStep()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1277, in evaluateStep
Eig1 = np.linalg.eigh(self.H)[0]
File "<__array_function__ internals>", line 6, in eigh
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 1471, in eigh
w, vt = gufunc(a, signature=signature, extobj=extobj)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 94, in _raise_linalgerror_eigenvalues_nonconvergence
raise LinAlgError("Eigenvalues did not converge")
numpy.linalg.LinAlgError: Eigenvalues did not converge


ids :
{'28816920'}
-------------------------------------
-------------------------------------
count : 1

Caught Executor Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.


ids :
{'28353283'}
-------------------------------------
-------------------------------------
count : 1

Caught Executor Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.


ids :
{'28394981'}
-------------------------------------

QCSubmit version information(click to expand)

	version
qcsubmit	v0.1.0
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

openff-dangerbot · 2020-11-07T12:32:00Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-11-07 12:32 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	ERROR
gfn2xtb	480	1	0
gfn1xtb	480	1	0
gfnff	321	4	156

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	32575	1	0
gfn1xtb	34205	1	0
gfnff	21927	29	896

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 863

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/programs/xtb.py", line 72, in compute
output = run_qcschema(input_data)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/xtb/qcschema/harness.py", line 208, in run_qcschema
return qcel.models.AtomicResult(**ret_data, stdout=output)
File "pydantic/main.py", line 346, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for AtomicResult
return_result
cannot reshape array of size 1 into shape (3) (type=value_error)



ids :
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'28351111', '28351807', '28351834', '28351835', '28351836', '28351837',
'28351838', '28351839', '28351840', '28351841', '28351842', '28353283',
'28353284', '28353285', '28353286', '28353287', '28353288', '28355916',
'28355917', '28355918', '28355919', '28355920', '28363700', '28363701',
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'28520306', '28520307', '28520308', '28520309', '28520344', '28520348',
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'28520773', '28520774', '28520775', '28520798', '28520812', '28520813',
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'28521217', '28521218', '28521219', '28521220', '28521221', '28521222',
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'28521229', '28521230', '28521231', '28521232', '28521233', '28521234',
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'28521795', '28521796', '28521797', '28521799', '28521800', '28521801',
'28521802', '28521803', '28521804', '28521805', '28521806', '28521807',
'28521808', '28521811', '28521812', '28521813', '28521814', '28521815',
'28521816', '28521817', '28521818', '28521819', '28521820', '28521821',
'28521822', '28521823', '28521824', '28521825', '28521826', '28521829',
'28521830', '28521831', '28521832', '28521833', '28521834', '28521835',
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'28521856', '28521857', '28521858', '28521859', '28521860', '28521861',
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'28521949', '28521950', '28521951', '28521952', '28521953', '28521954',
'28521955', '28521956', '28521957', '28521958', '28521959', '28521960',
'28521979', '28521980', '28521981', '28521982', '28521983', '28521984',
'28521985', '28521986', '28521987', '28521988', '28521989', '28521990',
'28521991', '28521992', '28521993', '28521994', '28521995', '28521996',
'28521997', '28521998', '28521999', '28522000', '28522001', '28522002',
'28522003', '28522004', '28522005', '28522006', '28522007', '28522008',
'28522009', '28522011', '28522012', '28522013', '28522014', '28522015',
'28522016', '28522017', '28522018', '28522019', '28522020', '28522025',
'28522026', '28522027', '28522028', '28522029', '28522030', '28522031',
'28522032', '28522033', '28522034', '28522035', '28522036', '28522037',
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'28522096', '28522097', '28522098', '28522099', '28522100', '28522101',
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'28962889', '28962890', '28962891', '28962892', '28962893', '28962914',
'28962915', '28964105', '28964106', '28964107', '28964109', '28964128',
'28964129', '28964150', '28964168', '28964169', '28964170', '28964186',
'28964187', '28964188', '28964189', '28964190', '28964191', '28964200',
'28964234', '28964235', '28964236', '28967071', '28967072', '28967086',
'28967087', '28967088', '28967106', '28967113', '28967114', '28967115',
'28967116', '28968285', '28968286', '28968287', '28968288', '28968289',
'28968290', '28968291', '28968292', '28968293', '28968294', '28969249',
'28969250', '28969251', '28969270', '28969271', '28969272', '28969296',
'28969297', '28969298', '28969299', '28972982', '28972983', '28973000',
'28973065', '28973066', '28973067', '28973068', '28973078', '28973099',
'28973100', '28976147', '28976148', '28976149', '28976150', '28976151',
'28976152', '28976153', '28976154', '28976155', '28976202', '28977117',
'28977143', '28977168', '28977177', '28977178', '28977179', '28977218',
'28977219', '28977220', '28977233', '28978143', '28978169', '28978170',
'28978171', '28978184', '28978212', '28978213', '28978237', '28978238',
'28978239', '28978824', '28978825', '28978826', '28978841', '28978842',
'28978850', '28978851', '28978852', '28978853', '28978893', '28979237',
'28979238', '28979239', '28979240', '28979251', '28979290', '28979291',
'28979292', '28979293', '28979331', '28982358', '28982367', '28982368',
'28982369', '28982370', '28982371', '28982372', '28982373', '28982374',
'28982375', '28984978', '28984979', '28984980', '28984981', '28984982',
'28984983', '28984984', '28985016', '28985017', '28985052'}
-------------------------------------
-------------------------------------
count : 32

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1301, in optimizeGeometry
raise GeomOptNotConvergedError("Optimizer.optimizeGeometry() failed to converge.")
geometric.errors.GeomOptNotConvergedError: Optimizer.optimizeGeometry() failed to converge.


ids :
{'28394045', '28394046', '28394047', '28394048', '28394049', '28394343',
'28394344', '28394345', '28394346', '28394347', '28394869', '28394909',
'28394910', '28394911', '28394912', '28478411', '28478886', '28478903',
'28478937', '28478978', '28511180', '28511181', '28511182', '28511183',
'28511220', '28511221', '28511236', '28511237', '28511260', '28511261',
'28577239', '28577775'}
-------------------------------------
-------------------------------------
count : 1

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1299, in optimizeGeometry
self.evaluateStep()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1277, in evaluateStep
Eig1 = np.linalg.eigh(self.H)[0]
File "<__array_function__ internals>", line 6, in eigh
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 1471, in eigh
w, vt = gufunc(a, signature=signature, extobj=extobj)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 94, in _raise_linalgerror_eigenvalues_nonconvergence
raise LinAlgError("Eigenvalues did not converge")
numpy.linalg.LinAlgError: Eigenvalues did not converge


ids :
{'28816920'}
-------------------------------------

QCSubmit version information(click to expand)

	version
qcsubmit	v0.1.0
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

openff-dangerbot · 2020-11-08T12:33:56Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-11-08 12:33 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	ERROR
gfn2xtb	480	1	0
gfn1xtb	480	1	0
gfnff	321	4	156

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	32575	1	0
gfn1xtb	34205	1	0
gfnff	21927	30	895

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 863

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/programs/xtb.py", line 72, in compute
output = run_qcschema(input_data)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/xtb/qcschema/harness.py", line 208, in run_qcschema
return qcel.models.AtomicResult(**ret_data, stdout=output)
File "pydantic/main.py", line 346, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for AtomicResult
return_result
cannot reshape array of size 1 into shape (3) (type=value_error)



ids :
{'28348614', '28348615', '28348616', '28348618', '28348619', '28351111',
'28351807', '28351834', '28351835', '28351836', '28351837', '28351838',
'28351839', '28351840', '28351841', '28351842', '28353283', '28353284',
'28353285', '28353286', '28353287', '28353288', '28355916', '28355917',
'28355918', '28355919', '28355920', '28355921', '28363700', '28363701',
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'28496199', '28496200', '28496201', '28496202', '28510925', '28510926',
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'28510995', '28510996', '28510997', '28510998', '28511025', '28511026',
'28511030', '28511031', '28511032', '28511039', '28511040', '28511041',
'28511054', '28511055', '28511056', '28511057', '28511058', '28511059',
'28511071', '28511072', '28511073', '28511074', '28511088', '28511103',
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'28511416', '28511417', '28511418', '28511419', '28511420', '28511433',
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'28511594', '28511595', '28511596', '28511605', '28511614', '28511615',
'28511616', '28511617', '28511618', '28511619', '28511620', '28511621',
'28511622', '28511623', '28511624', '28511625', '28520161', '28520202',
'28520235', '28520236', '28520267', '28520268', '28520269', '28520270',
'28520271', '28520272', '28520273', '28520274', '28520275', '28520305',
'28520306', '28520307', '28520308', '28520309', '28520344', '28520348',
'28520415', '28520607', '28520638', '28520669', '28520670', '28520695',
'28520705', '28520737', '28520738', '28520743', '28520771', '28520772',
'28520773', '28520774', '28520775', '28520798', '28520812', '28520813',
'28520814', '28521103', '28521104', '28521105', '28521106', '28521107',
'28521108', '28521109', '28521110', '28521111', '28521143', '28521144',
'28521145', '28521146', '28521147', '28521148', '28521149', '28521150',
'28521151', '28521152', '28521155', '28521165', '28521166', '28521167',
'28521168', '28521169', '28521170', '28521171', '28521172', '28521173',
'28521174', '28521175', '28521176', '28521177', '28521179', '28521180',
'28521181', '28521182', '28521183', '28521184', '28521185', '28521186',
'28521187', '28521188', '28521189', '28521190', '28521191', '28521192',
'28521193', '28521194', '28521195', '28521196', '28521197', '28521198',
'28521199', '28521200', '28521202', '28521203', '28521204', '28521205',
'28521206', '28521207', '28521208', '28521209', '28521210', '28521211',
'28521217', '28521218', '28521219', '28521220', '28521221', '28521222',
'28521223', '28521224', '28521225', '28521226', '28521227', '28521228',
'28521229', '28521230', '28521231', '28521232', '28521233', '28521234',
'28521691', '28521692', '28521693', '28521694', '28521695', '28521696',
'28521697', '28521698', '28521699', '28521700', '28521705', '28521706',
'28521707', '28521708', '28521709', '28521710', '28521735', '28521736',
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'28521751', '28521752', '28521753', '28521754', '28521755', '28521756',
'28521757', '28521758', '28521759', '28521760', '28521761', '28521762',
'28521763', '28521764', '28521765', '28521766', '28521767', '28521768',
'28521777', '28521778', '28521779', '28521780', '28521781', '28521782',
'28521783', '28521784', '28521785', '28521786', '28521787', '28521788',
'28521789', '28521790', '28521791', '28521792', '28521793', '28521794',
'28521795', '28521796', '28521797', '28521799', '28521801', '28521802',
'28521803', '28521804', '28521805', '28521806', '28521807', '28521808',
'28521811', '28521812', '28521813', '28521814', '28521815', '28521816',
'28521817', '28521818', '28521819', '28521820', '28521821', '28521822',
'28521823', '28521824', '28521825', '28521826', '28521829', '28521830',
'28521831', '28521832', '28521833', '28521834', '28521835', '28521836',
'28521848', '28521849', '28521853', '28521854', '28521855', '28521856',
'28521857', '28521858', '28521859', '28521860', '28521861', '28521862',
'28521863', '28521864', '28521865', '28521866', '28521867', '28521868',
'28521869', '28521870', '28521871', '28521872', '28521873', '28521874',
'28521875', '28521876', '28521877', '28521907', '28521908', '28521909',
'28521910', '28521911', '28521912', '28521913', '28521914', '28521915',
'28521937', '28521938', '28521939', '28521940', '28521941', '28521942',
'28521943', '28521944', '28521945', '28521946', '28521947', '28521948',
'28521949', '28521950', '28521951', '28521952', '28521953', '28521954',
'28521955', '28521956', '28521957', '28521958', '28521959', '28521960',
'28521979', '28521980', '28521981', '28521982', '28521983', '28521984',
'28521985', '28521986', '28521987', '28521988', '28521989', '28521990',
'28521991', '28521992', '28521993', '28521994', '28521995', '28521996',
'28521997', '28521998', '28521999', '28522000', '28522001', '28522002',
'28522003', '28522004', '28522005', '28522006', '28522007', '28522008',
'28522009', '28522011', '28522012', '28522013', '28522014', '28522015',
'28522016', '28522017', '28522018', '28522019', '28522020', '28522025',
'28522026', '28522027', '28522028', '28522029', '28522030', '28522031',
'28522032', '28522033', '28522034', '28522035', '28522036', '28522037',
'28522038', '28522039', '28522040', '28522041', '28522042', '28522043',
'28522044', '28522045', '28522046', '28522047', '28522048', '28522049',
'28522050', '28522051', '28522052', '28522053', '28522054', '28522055',
'28522056', '28522057', '28522058', '28522059', '28522060', '28522061',
'28522062', '28522064', '28522065', '28522066', '28522067', '28522068',
'28522069', '28522070', '28522071', '28522072', '28522073', '28522075',
'28522076', '28522077', '28522078', '28522079', '28522080', '28522081',
'28522082', '28522083', '28522084', '28522087', '28522088', '28522089',
'28522090', '28522091', '28522092', '28522093', '28522094', '28522095',
'28522096', '28522097', '28522098', '28522099', '28522100', '28522101',
'28522102', '28522103', '28522104', '28522105', '28522106', '28522118',
'28522119', '28522120', '28522121', '28522122', '28522123', '28522124',
'28522125', '28522126', '28522127', '28578707', '28579455', '28579456',
'28579457', '28579458', '28579459', '28579460', '28579487', '28579825',
'28579826', '28580048', '28580049', '28580808', '28580809', '28580810',
'28580811', '28581369', '28581370', '28582537', '28582538', '28582539',
'28584020', '28584021', '28584022', '28584023', '28584966', '28584967',
'28584968', '28584969', '28588765', '28588766', '28588767', '28589142',
'28589143', '28589144', '28589659', '28589660', '28589661', '28590510',
'28593314', '28597880', '28597881', '28600467', '28600495', '28600498',
'28600499', '28600500', '28600501', '28600522', '28600523', '28600539',
'28600540', '28601205', '28601206', '28605809', '28605810', '28609727',
'28609728', '28609729', '28609730', '28962886', '28962887', '28962888',
'28962889', '28962890', '28962891', '28962892', '28962893', '28962914',
'28962915', '28964105', '28964106', '28964107', '28964109', '28964128',
'28964129', '28964150', '28964168', '28964169', '28964170', '28964186',
'28964187', '28964188', '28964189', '28964190', '28964191', '28964200',
'28964234', '28964235', '28964236', '28967071', '28967072', '28967086',
'28967087', '28967088', '28967106', '28967113', '28967114', '28967115',
'28967116', '28968285', '28968286', '28968287', '28968288', '28968289',
'28968290', '28968291', '28968292', '28968293', '28968294', '28969249',
'28969250', '28969251', '28969270', '28969271', '28969272', '28969296',
'28969297', '28969298', '28969299', '28972982', '28972983', '28973000',
'28973065', '28973066', '28973067', '28973068', '28973078', '28973099',
'28973100', '28976147', '28976148', '28976149', '28976150', '28976151',
'28976152', '28976153', '28976154', '28976155', '28976202', '28977117',
'28977143', '28977168', '28977177', '28977178', '28977179', '28977218',
'28977219', '28977220', '28977233', '28978143', '28978169', '28978170',
'28978171', '28978184', '28978212', '28978213', '28978237', '28978238',
'28978239', '28978824', '28978825', '28978826', '28978841', '28978842',
'28978850', '28978851', '28978852', '28978853', '28978893', '28979237',
'28979238', '28979239', '28979240', '28979251', '28979290', '28979291',
'28979292', '28979293', '28979331', '28982358', '28982367', '28982368',
'28982369', '28982370', '28982371', '28982372', '28982373', '28982374',
'28982375', '28984978', '28984979', '28984980', '28984981', '28984982',
'28984983', '28984984', '28985016', '28985017', '28985052'}
-------------------------------------
-------------------------------------
count : 31

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1301, in optimizeGeometry
raise GeomOptNotConvergedError("Optimizer.optimizeGeometry() failed to converge.")
geometric.errors.GeomOptNotConvergedError: Optimizer.optimizeGeometry() failed to converge.


ids :
{'28394045', '28394046', '28394048', '28394049', '28394343', '28394344',
'28394345', '28394346', '28394347', '28394869', '28394909', '28394910',
'28394911', '28394912', '28478411', '28478886', '28478903', '28478937',
'28478978', '28511180', '28511181', '28511182', '28511183', '28511220',
'28511221', '28511236', '28511237', '28511260', '28511261', '28577239',
'28577775'}
-------------------------------------
-------------------------------------
count : 1

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1299, in optimizeGeometry
self.evaluateStep()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1277, in evaluateStep
Eig1 = np.linalg.eigh(self.H)[0]
File "<__array_function__ internals>", line 6, in eigh
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 1471, in eigh
w, vt = gufunc(a, signature=signature, extobj=extobj)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 94, in _raise_linalgerror_eigenvalues_nonconvergence
raise LinAlgError("Eigenvalues did not converge")
numpy.linalg.LinAlgError: Eigenvalues did not converge


ids :
{'28816920'}
-------------------------------------

QCSubmit version information(click to expand)

	version
qcsubmit	v0.1.0
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

openff-dangerbot · 2020-11-09T12:35:54Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-11-09 12:35 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	ERROR
gfn2xtb	480	1	0
gfn1xtb	480	1	0
gfnff	321	4	156

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	32575	1	0
gfn1xtb	34205	1	0
gfnff	21927	31	894

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 860

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/programs/xtb.py", line 72, in compute
output = run_qcschema(input_data)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/xtb/qcschema/harness.py", line 208, in run_qcschema
return qcel.models.AtomicResult(**ret_data, stdout=output)
File "pydantic/main.py", line 346, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for AtomicResult
return_result
cannot reshape array of size 1 into shape (3) (type=value_error)



ids :
{'28348617', '28348618', '28351807', '28351834', '28351835', '28351836',
'28351837', '28351838', '28351839', '28351840', '28351841', '28351842',
'28353283', '28353284', '28353285', '28353286', '28353287', '28353288',
'28355916', '28355917', '28355918', '28355919', '28355920', '28355921',
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'28511335', '28511336', '28511337', '28511338', '28511390', '28511391',
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'28521111', '28521112', '28521143', '28521144', '28521145', '28521146',
'28521147', '28521148', '28521149', '28521150', '28521151', '28521152',
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'28521188', '28521189', '28521190', '28521191', '28521192', '28521193',
'28521194', '28521195', '28521196', '28521197', '28521198', '28521199',
'28521200', '28521202', '28521203', '28521204', '28521205', '28521206',
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'28521218', '28521219', '28521220', '28521221', '28521222', '28521223',
'28521224', '28521225', '28521226', '28521227', '28521228', '28521229',
'28521230', '28521231', '28521232', '28521233', '28521234', '28521691',
'28521692', '28521693', '28521694', '28521695', '28521696', '28521697',
'28521698', '28521699', '28521700', '28521705', '28521706', '28521707',
'28521708', '28521709', '28521710', '28521735', '28521736', '28521737',
'28521738', '28521741', '28521742', '28521743', '28521744', '28521745',
'28521746', '28521747', '28521748', '28521749', '28521750', '28521751',
'28521752', '28521753', '28521754', '28521755', '28521756', '28521757',
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'28521764', '28521765', '28521766', '28521767', '28521768', '28521777',
'28521778', '28521780', '28521781', '28521782', '28521783', '28521784',
'28521785', '28521786', '28521787', '28521788', '28521789', '28521790',
'28521791', '28521792', '28521793', '28521794', '28521795', '28521796',
'28521797', '28521799', '28521801', '28521802', '28521803', '28521804',
'28521805', '28521806', '28521807', '28521808', '28521811', '28521812',
'28521813', '28521814', '28521815', '28521816', '28521817', '28521818',
'28521819', '28521820', '28521821', '28521822', '28521823', '28521824',
'28521825', '28521826', '28521829', '28521830', '28521831', '28521832',
'28521833', '28521834', '28521835', '28521836', '28521848', '28521849',
'28521853', '28521854', '28521855', '28521856', '28521857', '28521858',
'28521859', '28521860', '28521861', '28521862', '28521863', '28521864',
'28521865', '28521866', '28521867', '28521868', '28521869', '28521870',
'28521871', '28521872', '28521873', '28521874', '28521875', '28521876',
'28521877', '28521907', '28521908', '28521909', '28521910', '28521911',
'28521912', '28521913', '28521914', '28521915', '28521937', '28521938',
'28521939', '28521940', '28521941', '28521942', '28521943', '28521944',
'28521945', '28521946', '28521947', '28521948', '28521949', '28521950',
'28521951', '28521952', '28521953', '28521954', '28521955', '28521956',
'28521957', '28521958', '28521959', '28521960', '28521979', '28521980',
'28521981', '28521982', '28521983', '28521984', '28521985', '28521986',
'28521987', '28521988', '28521989', '28521990', '28521991', '28521992',
'28521993', '28521994', '28521995', '28521996', '28521997', '28521998',
'28521999', '28522000', '28522001', '28522002', '28522003', '28522004',
'28522005', '28522006', '28522007', '28522008', '28522009', '28522011',
'28522012', '28522013', '28522014', '28522015', '28522016', '28522017',
'28522018', '28522019', '28522020', '28522025', '28522026', '28522027',
'28522028', '28522029', '28522030', '28522031', '28522032', '28522033',
'28522034', '28522035', '28522036', '28522037', '28522038', '28522039',
'28522040', '28522041', '28522042', '28522043', '28522044', '28522045',
'28522046', '28522047', '28522048', '28522049', '28522050', '28522051',
'28522052', '28522053', '28522054', '28522055', '28522057', '28522058',
'28522059', '28522060', '28522061', '28522062', '28522064', '28522065',
'28522066', '28522067', '28522068', '28522069', '28522070', '28522071',
'28522072', '28522073', '28522075', '28522076', '28522077', '28522078',
'28522079', '28522080', '28522081', '28522082', '28522083', '28522084',
'28522087', '28522088', '28522089', '28522090', '28522091', '28522092',
'28522093', '28522094', '28522095', '28522096', '28522097', '28522098',
'28522099', '28522100', '28522101', '28522102', '28522103', '28522104',
'28522105', '28522106', '28522118', '28522119', '28522120', '28522121',
'28522122', '28522123', '28522124', '28522125', '28522126', '28522127',
'28578707', '28579455', '28579456', '28579457', '28579458', '28579459',
'28579460', '28579487', '28579825', '28579826', '28580048', '28580049',
'28580808', '28580809', '28580810', '28580811', '28581369', '28581370',
'28582537', '28582538', '28582539', '28584020', '28584021', '28584022',
'28584023', '28584966', '28584967', '28584968', '28584969', '28588765',
'28588766', '28588767', '28589142', '28589143', '28589144', '28589659',
'28589660', '28589661', '28590510', '28593314', '28597880', '28597881',
'28600467', '28600495', '28600498', '28600499', '28600500', '28600501',
'28600522', '28600523', '28600539', '28600540', '28601205', '28601206',
'28605809', '28605810', '28609727', '28609728', '28609729', '28609730',
'28962886', '28962887', '28962888', '28962889', '28962890', '28962891',
'28962892', '28962893', '28962914', '28962915', '28964105', '28964106',
'28964107', '28964109', '28964128', '28964129', '28964150', '28964168',
'28964169', '28964170', '28964186', '28964187', '28964188', '28964189',
'28964190', '28964191', '28964200', '28964234', '28964235', '28964236',
'28967071', '28967072', '28967086', '28967087', '28967088', '28967106',
'28967113', '28967114', '28967115', '28967116', '28968285', '28968286',
'28968287', '28968288', '28968289', '28968290', '28968291', '28968292',
'28968293', '28968294', '28969249', '28969250', '28969251', '28969270',
'28969271', '28969272', '28969296', '28969297', '28969298', '28969299',
'28972982', '28972983', '28973000', '28973065', '28973066', '28973067',
'28973068', '28973078', '28973099', '28973100', '28976147', '28976148',
'28976149', '28976150', '28976151', '28976152', '28976153', '28976154',
'28976155', '28976202', '28977117', '28977143', '28977168', '28977177',
'28977178', '28977179', '28977218', '28977219', '28977220', '28977233',
'28978143', '28978169', '28978170', '28978171', '28978184', '28978212',
'28978213', '28978237', '28978238', '28978239', '28978824', '28978825',
'28978826', '28978841', '28978842', '28978850', '28978851', '28978852',
'28978853', '28978893', '28979237', '28979238', '28979239', '28979240',
'28979251', '28979290', '28979291', '28979292', '28979293', '28979331',
'28982358', '28982367', '28982368', '28982369', '28982370', '28982371',
'28982372', '28982373', '28982374', '28982375', '28984978', '28984979',
'28984980', '28984981', '28984982', '28984983', '28984984', '28985016',
'28985017', '28985052'}
-------------------------------------
-------------------------------------
count : 30

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1301, in optimizeGeometry
raise GeomOptNotConvergedError("Optimizer.optimizeGeometry() failed to converge.")
geometric.errors.GeomOptNotConvergedError: Optimizer.optimizeGeometry() failed to converge.


ids :
{'28394045', '28394046', '28394047', '28394048', '28394343', '28394344',
'28394345', '28394346', '28394347', '28394869', '28394909', '28394910',
'28394911', '28394912', '28478411', '28478886', '28478903', '28478937',
'28478978', '28511180', '28511181', '28511182', '28511183', '28511220',
'28511221', '28511237', '28511260', '28511261', '28577239', '28577775'}
-------------------------------------
-------------------------------------
count : 2

Caught Executor Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.


ids :
{'28394989', '28496073'}
-------------------------------------
-------------------------------------
count : 1

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1299, in optimizeGeometry
self.evaluateStep()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1277, in evaluateStep
Eig1 = np.linalg.eigh(self.H)[0]
File "<__array_function__ internals>", line 6, in eigh
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 1471, in eigh
w, vt = gufunc(a, signature=signature, extobj=extobj)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 94, in _raise_linalgerror_eigenvalues_nonconvergence
raise LinAlgError("Eigenvalues did not converge")
numpy.linalg.LinAlgError: Eigenvalues did not converge


ids :
{'28816920'}
-------------------------------------
-------------------------------------
count : 1

Caught Executor Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.


ids :
{'28521800'}
-------------------------------------

QCSubmit version information(click to expand)

	version
qcsubmit	v0.1.0
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

openff-dangerbot · 2020-11-10T12:30:47Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-11-10 12:30 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	ERROR
gfn2xtb	480	1	0
gfn1xtb	480	0	1
gfnff	321	4	156

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	32575	1	0
gfn1xtb	34205	0	1
gfnff	21927	25	900

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 866

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/programs/xtb.py", line 72, in compute
output = run_qcschema(input_data)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/xtb/qcschema/harness.py", line 208, in run_qcschema
return qcel.models.AtomicResult(**ret_data, stdout=output)
File "pydantic/main.py", line 346, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for AtomicResult
return_result
cannot reshape array of size 1 into shape (3) (type=value_error)



ids :
{'28348614', '28348615', '28348616', '28348617', '28348618', '28351807',
'28351834', '28351835', '28351836', '28351837', '28351838', '28351839',
'28351840', '28351841', '28351842', '28353283', '28353284', '28353285',
'28353286', '28353287', '28353288', '28355916', '28355917', '28355918',
'28355919', '28355920', '28355921', '28363700', '28363701', '28363702',
'28363703', '28363704', '28363705', '28363706', '28363707', '28363708',
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'28398627', '28477648', '28477766', '28477803', '28477813', '28477863',
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'28510993', '28510994', '28510995', '28510996', '28510997', '28510998',
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'28521204', '28521205', '28521206', '28521207', '28521208', '28521209',
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'28521233', '28521234', '28521691', '28521692', '28521693', '28521694',
'28521695', '28521696', '28521697', '28521698', '28521699', '28521700',
'28521705', '28521706', '28521707', '28521708', '28521709', '28521710',
'28521735', '28521736', '28521737', '28521738', '28521741', '28521742',
'28521743', '28521744', '28521745', '28521746', '28521747', '28521748',
'28521749', '28521750', '28521751', '28521752', '28521753', '28521754',
'28521755', '28521756', '28521757', '28521758', '28521759', '28521760',
'28521761', '28521762', '28521763', '28521764', '28521765', '28521766',
'28521767', '28521768', '28521777', '28521778', '28521779', '28521780',
'28521781', '28521782', '28521783', '28521784', '28521785', '28521786',
'28521787', '28521788', '28521789', '28521790', '28521791', '28521792',
'28521793', '28521794', '28521795', '28521796', '28521797', '28521799',
'28521800', '28521801', '28521802', '28521803', '28521804', '28521805',
'28521806', '28521807', '28521808', '28521811', '28521812', '28521813',
'28521814', '28521815', '28521816', '28521817', '28521818', '28521819',
'28521820', '28521821', '28521822', '28521823', '28521824', '28521825',
'28521826', '28521829', '28521830', '28521831', '28521832', '28521833',
'28521834', '28521835', '28521836', '28521848', '28521849', '28521853',
'28521854', '28521855', '28521856', '28521857', '28521858', '28521859',
'28521860', '28521861', '28521862', '28521863', '28521864', '28521865',
'28521866', '28521867', '28521868', '28521869', '28521870', '28521871',
'28521872', '28521873', '28521874', '28521875', '28521876', '28521877',
'28521907', '28521908', '28521909', '28521910', '28521911', '28521912',
'28521913', '28521914', '28521915', '28521937', '28521938', '28521939',
'28521940', '28521941', '28521942', '28521943', '28521944', '28521945',
'28521946', '28521947', '28521948', '28521949', '28521950', '28521951',
'28521952', '28521953', '28521954', '28521955', '28521956', '28521957',
'28521958', '28521959', '28521960', '28521979', '28521980', '28521981',
'28521982', '28521983', '28521984', '28521985', '28521986', '28521987',
'28521988', '28521989', '28521990', '28521991', '28521992', '28521993',
'28521994', '28521995', '28521996', '28521997', '28521998', '28521999',
'28522000', '28522001', '28522002', '28522003', '28522004', '28522005',
'28522006', '28522007', '28522008', '28522009', '28522011', '28522012',
'28522013', '28522014', '28522015', '28522016', '28522017', '28522018',
'28522019', '28522020', '28522025', '28522026', '28522027', '28522028',
'28522029', '28522030', '28522031', '28522032', '28522033', '28522034',
'28522035', '28522036', '28522037', '28522038', '28522039', '28522040',
'28522041', '28522042', '28522043', '28522044', '28522045', '28522046',
'28522047', '28522048', '28522049', '28522050', '28522051', '28522052',
'28522053', '28522054', '28522055', '28522056', '28522057', '28522058',
'28522059', '28522060', '28522061', '28522062', '28522064', '28522065',
'28522066', '28522067', '28522068', '28522069', '28522070', '28522071',
'28522072', '28522073', '28522075', '28522076', '28522077', '28522078',
'28522079', '28522080', '28522081', '28522082', '28522083', '28522084',
'28522087', '28522088', '28522089', '28522090', '28522091', '28522092',
'28522093', '28522094', '28522095', '28522096', '28522097', '28522098',
'28522099', '28522100', '28522101', '28522102', '28522103', '28522104',
'28522105', '28522106', '28522118', '28522119', '28522120', '28522121',
'28522122', '28522123', '28522124', '28522125', '28522126', '28522127',
'28578707', '28579455', '28579456', '28579457', '28579458', '28579459',
'28579460', '28579487', '28579825', '28579826', '28580048', '28580049',
'28580808', '28580809', '28580810', '28580811', '28581369', '28581370',
'28582537', '28582538', '28582539', '28584020', '28584021', '28584022',
'28584023', '28584966', '28584967', '28584968', '28584969', '28588765',
'28588766', '28588767', '28589142', '28589143', '28589144', '28589659',
'28589660', '28589661', '28590510', '28593314', '28597880', '28597881',
'28600467', '28600495', '28600498', '28600499', '28600500', '28600501',
'28600522', '28600523', '28600539', '28600540', '28601205', '28601206',
'28605809', '28605810', '28609727', '28609728', '28609729', '28609730',
'28962886', '28962887', '28962888', '28962889', '28962890', '28962891',
'28962892', '28962893', '28962914', '28962915', '28964105', '28964106',
'28964107', '28964109', '28964128', '28964129', '28964150', '28964168',
'28964169', '28964170', '28964186', '28964187', '28964188', '28964189',
'28964190', '28964191', '28964200', '28964234', '28964235', '28964236',
'28967071', '28967072', '28967086', '28967087', '28967088', '28967106',
'28967113', '28967114', '28967115', '28967116', '28968285', '28968286',
'28968287', '28968288', '28968289', '28968290', '28968291', '28968292',
'28968293', '28968294', '28969249', '28969250', '28969251', '28969270',
'28969271', '28969272', '28969296', '28969297', '28969298', '28969299',
'28972982', '28972983', '28973000', '28973065', '28973066', '28973067',
'28973068', '28973078', '28973099', '28973100', '28976147', '28976148',
'28976149', '28976150', '28976151', '28976152', '28976153', '28976154',
'28976155', '28976202', '28977117', '28977143', '28977168', '28977177',
'28977178', '28977179', '28977218', '28977219', '28977220', '28977233',
'28978143', '28978169', '28978170', '28978171', '28978184', '28978212',
'28978213', '28978237', '28978238', '28978239', '28978824', '28978825',
'28978826', '28978841', '28978842', '28978850', '28978851', '28978852',
'28978853', '28978893', '28979237', '28979238', '28979239', '28979240',
'28979251', '28979290', '28979291', '28979292', '28979293', '28979331',
'28982358', '28982367', '28982368', '28982369', '28982370', '28982371',
'28982372', '28982373', '28982374', '28982375', '28984978', '28984979',
'28984980', '28984981', '28984982', '28984983', '28984984', '28985016',
'28985017', '28985052'}
-------------------------------------
-------------------------------------
count : 31

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1301, in optimizeGeometry
raise GeomOptNotConvergedError("Optimizer.optimizeGeometry() failed to converge.")
geometric.errors.GeomOptNotConvergedError: Optimizer.optimizeGeometry() failed to converge.


ids :
{'28394045', '28394046', '28394047', '28394048', '28394049', '28394343',
'28394344', '28394345', '28394346', '28394347', '28394869', '28394909',
'28394910', '28394911', '28394912', '28478411', '28478886', '28478903',
'28478937', '28478978', '28511180', '28511181', '28511182', '28511183',
'28511220', '28511221', '28511237', '28511260', '28511261', '28577239',
'28577775'}
-------------------------------------
-------------------------------------
count : 1

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1299, in optimizeGeometry
self.evaluateStep()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1277, in evaluateStep
Eig1 = np.linalg.eigh(self.H)[0]
File "<__array_function__ internals>", line 6, in eigh
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 1471, in eigh
w, vt = gufunc(a, signature=signature, extobj=extobj)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 94, in _raise_linalgerror_eigenvalues_nonconvergence
raise LinAlgError("Eigenvalues did not converge")
numpy.linalg.LinAlgError: Eigenvalues did not converge


ids :
{'28816920'}
-------------------------------------
-------------------------------------
count : 1

Caught Executor Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.


ids :
{'27816117'}
-------------------------------------
-------------------------------------
count : 1

Caught Executor Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.


ids :
{'28351111'}
-------------------------------------
-------------------------------------
count : 1

Caught Executor Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.


ids :
{'28511236'}
-------------------------------------

QCSubmit version information(click to expand)

	version
qcsubmit	v0.1.0
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

openff-dangerbot · 2020-11-11T12:33:09Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-11-11 12:33 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	ERROR
gfn2xtb	480	1	0
gfn1xtb	480	1	0
gfnff	321	4	156

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	32575	1	0
gfn1xtb	34205	1	0
gfnff	21927	29	896

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 863

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/programs/xtb.py", line 72, in compute
output = run_qcschema(input_data)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/xtb/qcschema/harness.py", line 208, in run_qcschema
return qcel.models.AtomicResult(**ret_data, stdout=output)
File "pydantic/main.py", line 346, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for AtomicResult
return_result
cannot reshape array of size 1 into shape (3) (type=value_error)



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'28521857', '28521858', '28521859', '28521860', '28521861', '28521862',
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'28964187', '28964188', '28964189', '28964190', '28964191', '28964200',
'28964234', '28964235', '28964236', '28967071', '28967072', '28967086',
'28967087', '28967088', '28967106', '28967113', '28967114', '28967115',
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'28968290', '28968291', '28968292', '28968293', '28968294', '28969249',
'28969250', '28969251', '28969270', '28969271', '28969272', '28969296',
'28969297', '28969298', '28969299', '28972982', '28972983', '28973000',
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'28973100', '28976147', '28976148', '28976149', '28976150', '28976151',
'28976152', '28976153', '28976154', '28976155', '28976202', '28977117',
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'28977219', '28977220', '28977233', '28978143', '28978169', '28978170',
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'28978239', '28978824', '28978825', '28978826', '28978841', '28978842',
'28978850', '28978851', '28978852', '28978853', '28978893', '28979237',
'28979238', '28979239', '28979240', '28979251', '28979290', '28979291',
'28979292', '28979293', '28979331', '28982358', '28982367', '28982368',
'28982369', '28982370', '28982371', '28982372', '28982373', '28982374',
'28982375', '28984978', '28984979', '28984980', '28984981', '28984982',
'28984983', '28984984', '28985016', '28985017', '28985052'}
-------------------------------------
-------------------------------------
count : 32

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1301, in optimizeGeometry
raise GeomOptNotConvergedError("Optimizer.optimizeGeometry() failed to converge.")
geometric.errors.GeomOptNotConvergedError: Optimizer.optimizeGeometry() failed to converge.


ids :
{'28394045', '28394046', '28394047', '28394048', '28394049', '28394343',
'28394344', '28394345', '28394346', '28394347', '28394869', '28394909',
'28394910', '28394911', '28394912', '28478411', '28478886', '28478903',
'28478937', '28478978', '28511180', '28511181', '28511182', '28511183',
'28511220', '28511221', '28511236', '28511237', '28511260', '28511261',
'28577239', '28577775'}
-------------------------------------
-------------------------------------
count : 1

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1299, in optimizeGeometry
self.evaluateStep()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1277, in evaluateStep
Eig1 = np.linalg.eigh(self.H)[0]
File "<__array_function__ internals>", line 6, in eigh
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 1471, in eigh
w, vt = gufunc(a, signature=signature, extobj=extobj)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 94, in _raise_linalgerror_eigenvalues_nonconvergence
raise LinAlgError("Eigenvalues did not converge")
numpy.linalg.LinAlgError: Eigenvalues did not converge


ids :
{'28816920'}
-------------------------------------

QCSubmit version information(click to expand)

	version
qcsubmit	v0.1.0
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

openff-dangerbot · 2020-11-12T12:31:38Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-11-12 12:31 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	ERROR
gfn2xtb	480	1	0
gfn1xtb	480	1	0
gfnff	321	159	1

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	32575	1	0
gfn1xtb	34205	1	0
gfnff	21927	924	1

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 1

Caught Executor Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.


ids :
{'28511332'}
-------------------------------------

QCSubmit version information(click to expand)

	version
qcsubmit	v0.1.0
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

openff-dangerbot · 2020-11-13T12:30:17Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-11-13 12:30 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	ERROR
gfn2xtb	480	1	0
gfn1xtb	480	1	0
gfnff	321	159	1

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	32575	1	0
gfn1xtb	34205	1	0
gfnff	21927	924	1

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 1

Caught Executor Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcfractal/queue/executor_adapter.py", line 15, in _get_future
return future.result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.


ids :
{'28511595'}
-------------------------------------

QCSubmit version information(click to expand)

	version
qcsubmit	v0.1.0
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

openff-dangerbot · 2020-11-14T12:34:58Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-11-14 12:34 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING
gfn2xtb	480	1
gfn1xtb	480	1
gfnff	321	160

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
gfn2xtb	32575	1
gfn1xtb	34205	1
gfnff	21927	925

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
qcsubmit	v0.1.0
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

openff-dangerbot · 2020-11-15T12:33:20Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-11-15 12:33 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	ERROR
gfn2xtb	480	1	0
gfn1xtb	480	1	0
gfnff	321	34	126

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	32575	1	0
gfn1xtb	34205	1	0
gfnff	21927	263	662

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 662

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/programs/xtb.py", line 72, in compute
output = run_qcschema(input_data)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/xtb/qcschema/harness.py", line 208, in run_qcschema
return qcel.models.AtomicResult(**ret_data, stdout=output)
File "pydantic/main.py", line 362, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for AtomicResult
return_result
cannot reshape array of size 1 into shape (3) (type=value_error)



ids :
{'28348615', '28348616', '28348617', '28348618', '28348619', '28351111',
'28351807', '28351834', '28351835', '28351836', '28351837', '28351838',
'28351839', '28351840', '28351841', '28351842', '28353283', '28353284',
'28353285', '28353286', '28353287', '28353288', '28355916', '28355917',
'28355918', '28355919', '28355920', '28355921', '28363700', '28363701',
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'28383951', '28383952', '28383953', '28383954', '28383955', '28383956',
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'28387074', '28387075', '28389309', '28389310', '28389311', '28389312',
'28389313', '28389314', '28389315', '28389316', '28394982', '28394983',
'28394984', '28394985', '28394986', '28394987', '28394988', '28394989',
'28397842', '28397843', '28397844', '28397845', '28397846', '28397847',
'28397848', '28398182', '28398183', '28398184', '28398185', '28398211',
'28398212', '28398622', '28398623', '28398624', '28398625', '28398626',
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'28479117', '28479118', '28479119', '28479120', '28496077', '28496078',
'28496079', '28496080', '28496081', '28496082', '28496083', '28496134',
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'28510996', '28510997', '28510998', '28511025', '28511026', '28511030',
'28511031', '28511032', '28511039', '28511040', '28511041', '28511054',
'28511055', '28511056', '28511057', '28511058', '28511059', '28511071',
'28511072', '28511073', '28511074', '28511088', '28511103', '28511104',
'28511114', '28511137', '28511150', '28511161', '28511162', '28511163',
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'28511334', '28511335', '28511336', '28511337', '28511338', '28511390',
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'28511457', '28511458', '28511459', '28511460', '28511461', '28511462',
'28511463', '28511464', '28511465', '28511466', '28511467', '28511494',
'28511557', '28511559', '28511593', '28511594', '28511595', '28511596',
'28511605', '28511614', '28511615', '28511616', '28511617', '28511618',
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'28511625', '28520161', '28520202', '28520235', '28520236', '28520267',
'28520268', '28520269', '28520270', '28520271', '28520272', '28520273',
'28520274', '28520275', '28520305', '28520306', '28520307', '28520309',
'28520344', '28520348', '28520415', '28520607', '28520638', '28520669',
'28520670', '28520695', '28520705', '28520737', '28520738', '28520743',
'28520771', '28520772', '28520773', '28520774', '28520775', '28520798',
'28520812', '28520813', '28520814', '28521103', '28521104', '28521105',
'28521106', '28521107', '28521108', '28521109', '28521110', '28521111',
'28521112', '28521143', '28521144', '28521145', '28521146', '28521147',
'28521148', '28521149', '28521150', '28521151', '28521152', '28521155',
'28521165', '28521166', '28521167', '28521168', '28521169', '28521170',
'28521171', '28521172', '28521173', '28521174', '28521175', '28521176',
'28521177', '28521178', '28521179', '28521180', '28521181', '28521182',
'28521183', '28521184', '28521185', '28521187', '28521188', '28521189',
'28521190', '28521191', '28521192', '28521193', '28521194', '28521195',
'28521196', '28521197', '28521198', '28521199', '28521200', '28521202',
'28521203', '28521204', '28521205', '28521206', '28521207', '28521208',
'28521209', '28521210', '28521211', '28521217', '28521220', '28521221',
'28521222', '28521223', '28521224', '28521225', '28521226', '28521227',
'28521228', '28521229', '28521230', '28521231', '28521233', '28521234',
'28521691', '28521692', '28521693', '28521694', '28521695', '28521696',
'28521697', '28521698', '28521699', '28521700', '28521705', '28521706',
'28521707', '28521708', '28521709', '28521710', '28521735', '28521736',
'28521737', '28521738', '28521742', '28521743', '28521744', '28521745',
'28521746', '28521747', '28521748', '28521749', '28521750', '28521751',
'28521752', '28521753', '28521755', '28521756', '28521757', '28521758',
'28521759', '28521760', '28521761', '28521762', '28521763', '28521764',
'28521765', '28521766', '28521767', '28521768', '28521777', '28521778',
'28521779', '28521780', '28521781', '28521782', '28521783', '28521784',
'28521786', '28521787', '28521788', '28521789', '28521790', '28521791',
'28521792', '28521793', '28521794', '28521795', '28521796', '28521797',
'28521799', '28521800', '28521801', '28521802', '28521803', '28521805',
'28521806', '28521807', '28521811', '28521812', '28521813', '28521814',
'28521815', '28521816', '28521817', '28521818', '28521819', '28521820',
'28521821', '28521822', '28521823', '28521824', '28521825', '28521826',
'28521829', '28521830', '28521831', '28521832', '28521833', '28521834',
'28521835', '28521836', '28521848', '28521849', '28521853', '28521854',
'28521855', '28521856', '28521857', '28521858', '28521859', '28521860',
'28521861', '28521862', '28521863', '28521866', '28521867', '28521868',
'28521869', '28521870', '28521871', '28521872', '28521873', '28521874',
'28521875', '28521876', '28521877', '28521907', '28521908', '28521909',
'28521910', '28521911', '28521912', '28521913', '28521914', '28521915',
'28521937', '28521938', '28521939', '28521940', '28521941', '28521942',
'28521943', '28521944', '28521945', '28521946', '28521947', '28521948',
'28521949', '28521951', '28521952', '28521953', '28521954', '28521955',
'28521956', '28521957', '28521958', '28521959', '28521960', '28521979',
'28521980', '28521982', '28521983', '28521985', '28521986', '28521988',
'28521989', '28521990', '28521991', '28521992', '28521993', '28521995',
'28521996', '28521997', '28521998', '28521999', '28522001', '28522002',
'28522003', '28522004', '28522005', '28522006', '28522007', '28522008',
'28522011', '28522012', '28522013', '28522014', '28522015', '28522016',
'28522017', '28522019', '28522020', '28522025', '28522026', '28522027',
'28522029', '28522030', '28522031', '28522032', '28522033', '28522035',
'28522036', '28522037', '28522038', '28522039', '28522040', '28522041',
'28522042', '28522043', '28522045', '28522046', '28522047', '28522048',
'28522050', '28522053', '28522054', '28522055', '28522056', '28522057',
'28522058', '28522059', '28522061', '28522062', '28522064', '28522066',
'28522067', '28522068', '28522069', '28522070', '28522072', '28522073',
'28522075', '28522077', '28522078', '28522079', '28522080', '28522082',
'28522084', '28522088', '28522089', '28522090', '28522092', '28522093',
'28522095', '28522096', '28522097', '28522098', '28522099', '28522100',
'28522102', '28522104', '28522105', '28522106', '28522119', '28522120',
'28522121', '28522123', '28522124', '28522125', '28522126', '28522127',
'28579455', '28579456', '28579457', '28579459', '28579460', '28579487',
'28579825', '28580048', '28580049', '28580808', '28580809', '28580810',
'28580811', '28581369', '28581370', '28582538', '28582539', '28584020',
'28584021', '28584023', '28584967', '28584968', '28588765', '28588767',
'28589142', '28589143', '28589144', '28589659', '28589660', '28589661',
'28590510', '28597880', '28597881', '28600495', '28600498', '28600500',
'28600539', '28609727'}
-------------------------------------

QCSubmit version information(click to expand)

	version
qcsubmit	v0.1.0
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

openff-dangerbot · 2020-11-16T12:59:20Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-11-16 12:59 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	ERROR
gfn2xtb	480	1	0
gfn1xtb	480	1	0
gfnff	324	1	156

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	32575	1	0
gfn1xtb	34205	1	0
gfnff	22029	4	901

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 868

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/programs/xtb.py", line 72, in compute
output = run_qcschema(input_data)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/xtb/qcschema/harness.py", line 208, in run_qcschema
return qcel.models.AtomicResult(**ret_data, stdout=output)
File "pydantic/main.py", line 362, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for AtomicResult
return_result
cannot reshape array of size 1 into shape (3) (type=value_error)



ids :
{'28348615', '28348616', '28348617', '28348618', '28348619', '28351111',
'28351807', '28351834', '28351835', '28351836', '28351837', '28351838',
'28351839', '28351840', '28351841', '28351842', '28353283', '28353284',
'28353285', '28353286', '28353287', '28353288', '28355916', '28355917',
'28355918', '28355919', '28355920', '28355921', '28363700', '28363701',
'28363702', '28363703', '28363704', '28363705', '28363706', '28363707',
'28363708', '28363709', '28383947', '28383948', '28383949', '28383950',
'28383951', '28383952', '28383953', '28383954', '28383955', '28383956',
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'28394988', '28394989', '28397842', '28397843', '28397844', '28397845',
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'28398625', '28398626', '28398627', '28477648', '28477766', '28477803',
'28477813', '28477863', '28477932', '28477969', '28478048', '28478049',
'28478092', '28478129', '28478156', '28478157', '28478158', '28478201',
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'28478451', '28478479', '28478556', '28478672', '28478698', '28478699',
'28478751', '28478806', '28478822', '28479017', '28479018', '28479019',
'28479064', '28479075', '28479084', '28479117', '28479118', '28479119',
'28479120', '28496077', '28496078', '28496079', '28496080', '28496081',
'28496082', '28496083', '28496134', '28496143', '28496144', '28496165',
'28496175', '28496198', '28496199', '28496200', '28496201', '28496202',
'28510925', '28510926', '28510942', '28510955', '28510974', '28510975',
'28510976', '28510988', '28510989', '28510990', '28510991', '28510992',
'28510993', '28510994', '28510995', '28510996', '28510997', '28510998',
'28511025', '28511026', '28511030', '28511031', '28511032', '28511039',
'28511040', '28511041', '28511054', '28511055', '28511056', '28511057',
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'28521911', '28521912', '28521913', '28521914', '28521915', '28521937',
'28521938', '28521939', '28521940', '28521941', '28521942', '28521943',
'28521944', '28521945', '28521946', '28521947', '28521948', '28521949',
'28521950', '28521951', '28521952', '28521953', '28521954', '28521955',
'28521956', '28521957', '28521958', '28521959', '28521960', '28521979',
'28521980', '28521981', '28521982', '28521983', '28521984', '28521985',
'28521986', '28521987', '28521988', '28521989', '28521990', '28521991',
'28521992', '28521993', '28521994', '28521995', '28521996', '28521997',
'28521998', '28521999', '28522000', '28522001', '28522002', '28522003',
'28522004', '28522005', '28522006', '28522007', '28522008', '28522009',
'28522011', '28522012', '28522013', '28522014', '28522015', '28522016',
'28522017', '28522018', '28522019', '28522020', '28522025', '28522026',
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'28522033', '28522034', '28522035', '28522036', '28522037', '28522038',
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'28522064', '28522065', '28522066', '28522067', '28522068', '28522069',
'28522070', '28522071', '28522072', '28522073', '28522075', '28522076',
'28522077', '28522078', '28522079', '28522080', '28522081', '28522082',
'28522083', '28522084', '28522087', '28522088', '28522089', '28522090',
'28522091', '28522092', '28522093', '28522094', '28522095', '28522096',
'28522097', '28522098', '28522099', '28522100', '28522101', '28522102',
'28522103', '28522104', '28522105', '28522106', '28522118', '28522119',
'28522120', '28522121', '28522122', '28522123', '28522124', '28522125',
'28522126', '28522127', '28578707', '28579455', '28579456', '28579457',
'28579458', '28579459', '28579460', '28579487', '28579825', '28579826',
'28580048', '28580049', '28580808', '28580809', '28580810', '28580811',
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'28584021', '28584022', '28584023', '28584966', '28584967', '28584968',
'28584969', '28588765', '28588766', '28588767', '28589142', '28589143',
'28589144', '28589659', '28589660', '28589661', '28590510', '28593314',
'28597880', '28597881', '28600467', '28600495', '28600498', '28600499',
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'28601205', '28601206', '28605809', '28605810', '28609727', '28609728',
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'28964105', '28964106', '28964107', '28964109', '28964128', '28964129',
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'28968285', '28968286', '28968287', '28968288', '28968289', '28968290',
'28968291', '28968292', '28968293', '28968294', '28969249', '28969250',
'28969251', '28969270', '28969271', '28969272', '28969296', '28969297',
'28969298', '28969299', '28972982', '28972983', '28973000', '28973065',
'28973066', '28973067', '28973068', '28973078', '28973099', '28973100',
'28976147', '28976148', '28976149', '28976150', '28976151', '28976152',
'28976153', '28976154', '28976155', '28976202', '28977117', '28977143',
'28977168', '28977177', '28977178', '28977179', '28977218', '28977219',
'28977220', '28977233', '28978143', '28978169', '28978170', '28978171',
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'28978824', '28978825', '28978826', '28978841', '28978842', '28978850',
'28978851', '28978852', '28978853', '28978893', '28979237', '28979238',
'28979239', '28979240', '28979251', '28979290', '28979291', '28979292',
'28979293', '28979331', '28982358', '28982367', '28982368', '28982369',
'28982370', '28982371', '28982372', '28982373', '28982374', '28982375',
'28984978', '28984979', '28984980', '28984981', '28984982', '28984983',
'28984984', '28985016', '28985017', '28985052'}
-------------------------------------
-------------------------------------
count : 32

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1301, in optimizeGeometry
raise GeomOptNotConvergedError("Optimizer.optimizeGeometry() failed to converge.")
geometric.errors.GeomOptNotConvergedError: Optimizer.optimizeGeometry() failed to converge.


ids :
{'28394045', '28394046', '28394047', '28394048', '28394049', '28394343',
'28394344', '28394345', '28394346', '28394347', '28394869', '28394909',
'28394910', '28394911', '28394912', '28478411', '28478886', '28478903',
'28478937', '28478978', '28511180', '28511181', '28511182', '28511183',
'28511220', '28511221', '28511236', '28511237', '28511260', '28511261',
'28577239', '28577775'}
-------------------------------------
-------------------------------------
count : 1

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1299, in optimizeGeometry
self.evaluateStep()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1277, in evaluateStep
Eig1 = np.linalg.eigh(self.H)[0]
File "<__array_function__ internals>", line 6, in eigh
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 1471, in eigh
w, vt = gufunc(a, signature=signature, extobj=extobj)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 94, in _raise_linalgerror_eigenvalues_nonconvergence
raise LinAlgError("Eigenvalues did not converge")
numpy.linalg.LinAlgError: Eigenvalues did not converge


ids :
{'28816920'}
-------------------------------------

QCSubmit version information(click to expand)

	version
qcsubmit	v0.1.0
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

openff-dangerbot · 2020-11-17T14:44:43Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-11-17 14:44 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING	ERROR
gfn2xtb	480	1	0
gfn1xtb	480	1	0
gfnff	324	2	155

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
gfn2xtb	32575	1	0
gfn1xtb	34205	1	0
gfnff	22069	5	900

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 868

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/qcengine/programs/xtb.py", line 72, in compute
output = run_qcschema(input_data)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/xtb/qcschema/harness.py", line 208, in run_qcschema
return qcel.models.AtomicResult(**ret_data, stdout=output)
File "pydantic/main.py", line 362, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for AtomicResult
return_result
cannot reshape array of size 1 into shape (3) (type=value_error)



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'28520771', '28520772', '28520773', '28520774', '28520775', '28520798',
'28520812', '28520813', '28520814', '28521103', '28521104', '28521105',
'28521106', '28521107', '28521108', '28521109', '28521110', '28521111',
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'28984984', '28985016', '28985017', '28985052'}
-------------------------------------
-------------------------------------
count : 32

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 225, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/chodera/miniconda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1301, in optimizeGeometry
raise GeomOptNotConvergedError("Optimizer.optimizeGeometry() failed to converge.")
geometric.errors.GeomOptNotConvergedError: Optimizer.optimizeGeometry() failed to converge.


ids :
{'28394045', '28394046', '28394047', '28394048', '28394049', '28394343',
'28394344', '28394345', '28394346', '28394347', '28394869', '28394909',
'28394910', '28394911', '28394912', '28478411', '28478886', '28478903',
'28478937', '28478978', '28511180', '28511181', '28511182', '28511183',
'28511220', '28511221', '28511236', '28511237', '28511260', '28511261',
'28577239', '28577775'}
-------------------------------------

QCSubmit version information(click to expand)

	version
qcsubmit	v0.1.0
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

openff-dangerbot · 2020-11-17T18:17:29Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-11-17 18:17 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING
gfn2xtb	480	1
gfn1xtb	480	1
gfnff	324	157

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
gfn2xtb	32575	1
gfn1xtb	34205	1
gfnff	22069	905

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
qcsubmit	v0.1.0
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

openff-dangerbot · 2020-11-18T12:36:37Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF-benchmark-ligand-fragments-v1.0
Dataset Type	TorsiondriveDataset
UTC Datetime	2020-11-18 12:36 UTC

All errored tasks and services will be restarted.
Errored states prior to restart reported below.

`TorsionDriveRecord` current status

specification	COMPLETE	RUNNING
gfn2xtb	480	1
gfn1xtb	480	1
gfnff	324	157

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
gfn2xtb	32575	1
gfn1xtb	34205	1
gfnff	22069	905

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
qcsubmit	v0.1.0
openforcefield	0.8.0
basis_set_exchange	v0.8.13
qcelemental	v0.17.0
rdkit	2020.09.1

dotsdl · 2020-11-19T00:13:50Z

@jthorton I'm going to move this to "Requires Scientific Review", as it appears the remaining gfnff optimizations are doomed to failure until grimme-lab/xtb-python#33 is resolved. I'm concerned about the remaining gfn2xtb and gfn1xtb optimizations. I can try retagging these and route to my debug box here.

Please let me know if this sounds reasonable to you.

xtb Compute for the fragmented ligand set.

jthorton added 2 commits October 12, 2020 14:57

Add compute for the xtb gfn1-2 and ff methods.

c5e5524

update the README with the extra compute details.

152a351

expand compute validation checking to hit any files like "compute*.json"

b301500

use basename on the full file path.

dd90c09

dotsdl self-requested a review October 13, 2020 15:22

dotsdl approved these changes Oct 13, 2020

View reviewed changes

dotsdl added the tracking label Oct 13, 2020

jthorton merged commit a6633e6 into master Oct 14, 2020

jthorton deleted the xtb_fragments branch November 3, 2020 15:59

dotsdl removed the tracking label Dec 7, 2021

dotsdl pushed a commit that referenced this pull request Feb 23, 2022

Merge pull request #146 from openforcefield/xtb_fragments

138ff7e

xtb Compute for the fragmented ligand set.

xtb Compute for the fragmented ligand set. #146

xtb Compute for the fragmented ligand set. #146

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jthorton commented Oct 12, 2020 • edited Loading

openff-dangerbot commented Oct 12, 2020

QCSubmit Validation Report

QC Specification Report

openff-dangerbot commented Oct 12, 2020

QCSubmit Validation Report

QC Specification Report

openff-dangerbot commented Oct 12, 2020

QCSubmit Validation Report

QC Specification Report

jthorton commented Oct 12, 2020

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openff-dangerbot commented Oct 14, 2020

Lifecycle - QCSubmit Submission Report : SUCCESS

openff-dangerbot commented Oct 14, 2020

Lifecycle - Error Cycling Report

TorsionDriveRecord current status

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dotsdl commented Oct 14, 2020

openff-dangerbot commented Oct 15, 2020

Lifecycle - Error Cycling Report

TorsionDriveRecord current status

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OptimizationRecord Error Tracebacks:

openff-dangerbot commented Oct 16, 2020

Lifecycle - Error Cycling Report

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openff-dangerbot commented Oct 17, 2020

Lifecycle - Error Cycling Report

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openff-dangerbot commented Oct 19, 2020

Lifecycle - Error Cycling Report

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openff-dangerbot commented Oct 19, 2020

Lifecycle - Error Cycling Report

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openff-dangerbot commented Oct 20, 2020

Lifecycle - Error Cycling Report

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openff-dangerbot commented Oct 21, 2020

Lifecycle - Error Cycling Report

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openff-dangerbot commented Oct 21, 2020

Lifecycle - Error Cycling Report

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openff-dangerbot commented Oct 22, 2020

Lifecycle - Error Cycling Report

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openff-dangerbot commented Oct 23, 2020

Lifecycle - Error Cycling Report

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openff-dangerbot commented Oct 24, 2020

Lifecycle - Error Cycling Report

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jthorton commented Oct 12, 2020 •

edited

Loading

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