Describe the bug
~20% of xtb calculations result in the error:
Traceback (most recent call last):
File "/opt/conda/envs/qcfractal/lib/python3.10/site-packages/qcfractalcompute/apps/helpers.py", line 81, in run_conda_subprocess
ret = json.loads(proc_result.stdout)
File "/opt/conda/envs/qcfractal/lib/python3.10/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
File "/opt/conda/envs/qcfractal/lib/python3.10/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/opt/conda/envs/qcfractal/lib/python3.10/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 2 column 2 (char 2)
To Reproduce
Rerun the following record
from qcportal import PortalClient
qc_client = PortalClient("[https://api.qcarchive.molssi.org:443/](https://api.qcarchive.molssi.org/)", cache_dir=".")
record = qc_client.get_records([145252038])[0]
print(record.error["error_message"])
Expected behavior
The output json file will read successfully
Additional context
The actual standard out seems to append the target json string to the xtb log output, where the latter cannot be processed as a json.
Error getting task result:
Traceback (most recent call last):
File "/opt/conda/envs/qcfractal/lib/python3.10/site-packages/qcfractalcompute/apps/helpers.py", line 81, in run_conda_subprocess
ret = json.loads(proc_result.stdout)
File "/opt/conda/envs/qcfractal/lib/python3.10/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
File "/opt/conda/envs/qcfractal/lib/python3.10/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/opt/conda/envs/qcfractal/lib/python3.10/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 2 column 2 (char 2)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/conda/envs/qcfractal/lib/python3.10/site-packages/qcfractalcompute/compute_manager.py", line 397, in _acquire_complete_tasks
ret[executor_label][task_id] = task.result()
File "/opt/conda/envs/qcfractal/lib/python3.10/concurrent/futures/_base.py", line 451, in result
return self.__get_result()
File "/opt/conda/envs/qcfractal/lib/python3.10/concurrent/futures/_base.py", line 403, in __get_result
raise self._exception
File "/opt/conda/envs/qcfractal/lib/python3.10/site-packages/parsl/dataflow/dflow.py", line 343, in handle_exec_update
res = self._unwrap_remote_exception_wrapper(future)
File "/opt/conda/envs/qcfractal/lib/python3.10/site-packages/parsl/dataflow/dflow.py", line 607, in _unwrap_remote_exception_wrapper
result.reraise()
File "/opt/conda/envs/qcfractal/lib/python3.10/site-packages/parsl/app/errors.py", line 114, in reraise
raise v
File "/opt/conda/envs/qcfractal/lib/python3.10/site-packages/parsl/app/errors.py", line 138, in wrapper
return func(*args, **kwargs)
File "/opt/conda/envs/qcfractal/lib/python3.10/site-packages/qcfractalcompute/apps/qcengine.py", line 46, in qcengine_conda_app
return run_conda_subprocess(conda_env_name, cmd, executor_config.scratch_directory, {})
File "/opt/conda/envs/qcfractal/lib/python3.10/site-packages/qcfractalcompute/apps/helpers.py", line 83, in run_conda_subprocess
raise RuntimeError(f"Failed to parse JSON from subprocess stdout: {proc_result.stdout}")
RuntimeError: Failed to parse JSON from subprocess stdout:
transition dipole moment (au) for excitation: 59 60
X Y Z
0.0742 0.2388 0.0696 total (au/Debye): 0.260 0.660
dE (eV) : 0.511
oscillator strength : 0.11928E-02
transition dipole moment (au) for excitation: 59 60
X Y Z
-0.0823 -0.2251 -0.0200 total (au/Debye): 0.241 0.611
dE (eV) : 0.489
oscillator strength : 0.98072E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
0.1087 0.1739 -0.0221 total (au/Debye): 0.206 0.524
dE (eV) : 0.488
oscillator strength : 0.71908E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
-0.1173 -0.1444 0.0333 total (au/Debye): 0.189 0.480
dE (eV) : 0.483
oscillator strength : 0.59779E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
-0.1183 -0.1347 0.0367 total (au/Debye): 0.183 0.465
dE (eV) : 0.480
oscillator strength : 0.55701E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
-0.1211 -0.1169 0.0385 total (au/Debye): 0.173 0.439
dE (eV) : 0.482
oscillator strength : 0.49755E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
-0.1230 -0.0846 0.0404 total (au/Debye): 0.155 0.393
dE (eV) : 0.485
oscillator strength : 0.40194E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
0.1145 0.0302 -0.0404 total (au/Debye): 0.125 0.318
dE (eV) : 0.474
oscillator strength : 0.25741E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
0.0682 -0.0811 -0.0409 total (au/Debye): 0.114 0.289
dE (eV) : 0.384
oscillator strength : 0.17155E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
0.0232 -0.1589 -0.0472 total (au/Debye): 0.167 0.426
dE (eV) : 0.293
oscillator strength : 0.28488E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
-0.0088 -0.1454 -0.0521 total (au/Debye): 0.155 0.393
dE (eV) : 0.226
oscillator strength : 0.18730E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
-0.0091 -0.1295 -0.0368 total (au/Debye): 0.135 0.343
dE (eV) : 0.240
oscillator strength : 0.15139E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
-0.0223 -0.2834 -0.0171 total (au/Debye): 0.285 0.724
dE (eV) : 0.238
oscillator strength : 0.66754E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
0.0127 0.2749 0.0291 total (au/Debye): 0.277 0.703
dE (eV) : 0.189
oscillator strength : 0.50179E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
0.0105 0.2497 0.0233 total (au/Debye): 0.251 0.638
dE (eV) : 0.187
oscillator strength : 0.40897E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
0.0052 0.2565 0.0140 total (au/Debye): 0.257 0.653
dE (eV) : 0.178
oscillator strength : 0.40778E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
-0.0012 0.2667 0.0060 total (au/Debye): 0.267 0.678
dE (eV) : 0.169
oscillator strength : 0.41758E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
0.0093 -0.2568 0.0033 total (au/Debye): 0.257 0.653
dE (eV) : 0.160
oscillator strength : 0.36647E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
0.0173 -0.2333 0.0101 total (au/Debye): 0.234 0.595
dE (eV) : 0.148
oscillator strength : 0.28170E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
-0.0174 0.2209 -0.0087 total (au/Debye): 0.222 0.564
dE (eV) : 0.143
oscillator strength : 0.24391E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
-0.0155 0.2325 -0.0031 total (au/Debye): 0.233 0.592
dE (eV) : 0.142
oscillator strength : 0.26757E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
-0.0134 0.2513 0.0018 total (au/Debye): 0.252 0.640
dE (eV) : 0.143
oscillator strength : 0.31289E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
-0.0115 0.2772 0.0067 total (au/Debye): 0.278 0.705
dE (eV) : 0.143
oscillator strength : 0.38167E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
-0.0091 0.2957 0.0106 total (au/Debye): 0.296 0.752
dE (eV) : 0.143
oscillator strength : 0.43335E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
-0.0082 0.3011 0.0111 total (au/Debye): 0.301 0.766
dE (eV) : 0.142
oscillator strength : 0.44706E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
-0.0074 0.2960 0.0107 total (au/Debye): 0.296 0.753
dE (eV) : 0.141
oscillator strength : 0.42960E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
-0.0076 0.2887 0.0092 total (au/Debye): 0.289 0.734
dE (eV) : 0.140
oscillator strength : 0.40603E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
-0.0074 0.2862 0.0088 total (au/Debye): 0.286 0.728
dE (eV) : 0.140
oscillator strength : 0.39796E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
-0.0072 0.2859 0.0087 total (au/Debye): 0.286 0.727
dE (eV) : 0.140
oscillator strength : 0.39643E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
-0.0071 0.2871 0.0088 total (au/Debye): 0.287 0.730
dE (eV) : 0.140
oscillator strength : 0.39925E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
-0.0069 0.2879 0.0090 total (au/Debye): 0.288 0.732
dE (eV) : 0.140
oscillator strength : 0.40170E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
-0.0068 0.2886 0.0091 total (au/Debye): 0.289 0.734
dE (eV) : 0.140
oscillator strength : 0.40415E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
-0.0066 0.2888 0.0091 total (au/Debye): 0.289 0.735
dE (eV) : 0.140
oscillator strength : 0.40575E-03
transition dipole moment (au) for excitation: 59 60
X Y Z
-0.0063 0.2884 0.0090 total (au/Debye): 0.289 0.734
dE (eV) : 0.141
oscillator strength : 0.40609E-03
{"id": "145252038", "hash_index": null, "schema_name": "qcschema_optimization_output....
Describe the bug
~20% of xtb calculations result in the error:
To Reproduce
Rerun the following record
Expected behavior
The output json file will read successfully
Additional context
The actual standard out seems to append the target json string to the xtb log output, where the latter cannot be processed as a json.