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Can I have some help running a test molecule #152

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xiki-tempula opened this issue Apr 4, 2022 · 5 comments
Closed

Can I have some help running a test molecule #152

xiki-tempula opened this issue Apr 4, 2022 · 5 comments

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@xiki-tempula
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Hi, I'm trying to run the default workflow on a test molecule but It failed. I wonder if I could have some help? Thank you.
The test molecule sdf is generated by openeye and is

  -OEChem-04042209103D
 xtb: 6.4.1 (conda-forge)
 32 33  0     0  0  0  0  0  0999 V2000
   -1.8741   21.5782  -27.4162 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3296   22.4662  -28.3280 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1178   22.9451  -29.3623 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4444   22.5460  -29.5022 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9674   21.6514  -28.5716 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1914   21.1698  -27.5282 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6139   21.1665  -28.7107 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -4.2810   23.0060  -30.6713 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6417   22.2517  -31.5407 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5595   24.3384  -30.6025 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2872   25.1170  -31.4989 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8992   24.6061  -32.6433 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5957   25.4895  -33.4480 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7178   26.7817  -33.1998 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1311   27.2639  -32.1070 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4044   26.4764  -31.2228 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3207   28.6307  -31.9389 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8773   29.4459  -30.9349 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2120   29.0687  -29.9987 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3155   30.8813  -31.1250 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4386   24.0448  -30.5124 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -7.4016   30.9398  -31.1493 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2641   21.2005  -26.6104 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3038   22.7865  -28.2443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6205   20.4817  -26.8182 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1740   24.8510  -29.8194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8296   23.5618  -32.8900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0891   25.1453  -34.3467 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9483   26.9175  -30.3525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8727   29.0355  -32.6844 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9228   31.2719  -32.0613 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9421   31.4820  -30.3010 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  1  6  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  4  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 11 16  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
  3 21  1  0  0  0  0
 20 22  1  0  0  0  0
  1 23  1  0  0  0  0
  2 24  1  0  0  0  0
  6 25  1  0  0  0  0
 10 26  1  0  0  0  0
 12 27  1  0  0  0  0
 13 28  1  0  0  0  0
 16 29  1  0  0  0  0
 17 30  1  0  0  0  0
 20 31  1  0  0  0  0
 20 32  1  0  0  0  0
M  END
$$$$

I created the env with mamba create -n bespokefit -c conda-forge -c openeye -c psi4 openeye-toolkits openff-bespokefit xtb-python torchani psi4
and generate the topology with openff-bespoke executor run --file "lig.sdf" --workflow "default" --output "acetaminophen.json" --output-force-field "acetaminophen.offxml" --n-qc-compute-workers 2 --qc-compute-n-cores 8

But I got the error of

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

[✓] bespoke executor launched

1. preparing the bespoke workflow                                                                                                                           
                                                                                                                                                            
[✓] 1 molecules found
[✓] fitting schemas generated
                                                                                                                                                            
2. submitting the workflow                                                                                                                                  
                                                                                                                                                            
[✓] the following workflows were submitted
┏━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━━┓
┃ ID ┃ SMILES                                ┃ NAME ┃ FILE    ┃
┡━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━╇━━━━━━━━━┩
│ 1  │ CC(=O)Nc1cc(ccn1)NC(=O)c2c(cccc2Cl)Cl │      │ lig.sdf │
└────┴───────────────────────────────────────┴──────┴─────────┘
                                                                                                                                                            
3. running the fitting pipeline                                                                                                                             
                                                                                                                                                            
[✓] fragmentation successful
[x] qc-generation failed
                                                                                                                                                            
 [{"type": "ValueError", "message": "TorsionDrive error at 0:\ngeomeTRIC run_json error:\nTraceback (most recent call last):\n  File                        
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/run_json.py\", line 225, in geometric_run_json\n                         
 geometric.optimize.Optimize(coords, M, IC, engine, None, params)\n  File                                                                                   
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 1331, in Optimize\n    return                        
 optimizer.optimizeGeometry()\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 1293, in        
 optimizeGeometry\n    self.calcEnergyForce()\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 
 1002, in calcEnergyForce\n    spcalc = self.engine.calc(self.X, self.dirname)\n  File                                                                      
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/engine.py\", line 873, in calc\n    return self.calc_new(coords,         
 dirname)\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/engine.py\", line 865, in calc_new\n    raise           
 QCEngineAPIEngineError(\"QCEngineAPI computation did not execute correctly. Message: \" +                                                                  
 ret[\"error\"][\"error_message\"])\ngeometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution
 Error:\nTraceback (most recent call last):\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/util.py\", line 114, in
 compute_wrapper\n    yield metadata\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/compute.py\", line 91, in     
 compute\n    output_data = executor.compute(input_data, config)\n  File                                                                                    
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/programs/psi4.py\", line 121, in compute\n    pversion =                  
 parse_version(self.get_version())\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/programs/psi4.py\", line 91, in 
 get_version\n    self.version_cache = safe_version(exc[\"stdout\"].split()[-1])\nIndexError: list index out of range\n\n", "traceback": "Traceback (most   
 recent call last):\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/celery/app/trace.py\", line 451, in trace_task\n    R = 
 retval = fun(*args, **kwargs)\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/celery/app/trace.py\", line 734, in          
 __protected_call__\n    return self.run(*args, **kwargs)\n  File                                                                                           
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/openff/bespokefit/executor/services/qcgenerator/worker.py\", line 132, in          
 compute_torsion_drive\n    return_value = qcengine.compute_procedure(\n  File                                                                              
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/compute.py\", line 149, in compute_procedure\n    return                  
 handle_output_metadata(output_data, metadata, raise_error=raise_error, return_dict=return_dict)\n  File                                                    
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/util.py\", line 177, in handle_output_metadata\n    raise                 
 ValueError(output_fusion[\"error\"][\"error_message\"])\nValueError: TorsionDrive error at 0:\ngeomeTRIC run_json error:\nTraceback (most recent call      
 last):\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/run_json.py\", line 225, in geometric_run_json\n          
 geometric.optimize.Optimize(coords, M, IC, engine, None, params)\n  File                                                                                   
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 1331, in Optimize\n    return                        
 optimizer.optimizeGeometry()\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 1293, in        
 optimizeGeometry\n    self.calcEnergyForce()\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 
 1002, in calcEnergyForce\n    spcalc = self.engine.calc(self.X, self.dirname)\n  File                                                                      
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/engine.py\", line 873, in calc\n    return self.calc_new(coords,         
 dirname)\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/engine.py\", line 865, in calc_new\n    raise           
 QCEngineAPIEngineError(\"QCEngineAPI computation did not execute correctly. Message: \" +                                                                  
 ret[\"error\"][\"error_message\"])\ngeometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution
 Error:\nTraceback (most recent call last):\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/util.py\", line 114, in
 compute_wrapper\n    yield metadata\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/compute.py\", line 91, in     
 compute\n    output_data = executor.compute(input_data, config)\n  File                                                                                    
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/programs/psi4.py\", line 121, in compute\n    pversion =                  
 parse_version(self.get_version())\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/programs/psi4.py\", line 91, in 
 get_version\n    self.version_cache = safe_version(exc[\"stdout\"].split()[-1])\nIndexError: list index out of range\n\n\n"}, {"type": "ValueError",       
 "message": "TorsionDrive error at 90:\ngeomeTRIC run_json error:\nTraceback (most recent call last):\n  File                                               
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/run_json.py\", line 225, in geometric_run_json\n                         
 geometric.optimize.Optimize(coords, M, IC, engine, None, params)\n  File                                                                                   
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 1331, in Optimize\n    return                        
 optimizer.optimizeGeometry()\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 1293, in        
 optimizeGeometry\n    self.calcEnergyForce()\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 
 1002, in calcEnergyForce\n    spcalc = self.engine.calc(self.X, self.dirname)\n  File                                                                      
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/engine.py\", line 873, in calc\n    return self.calc_new(coords,         
 dirname)\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/engine.py\", line 865, in calc_new\n    raise           
 QCEngineAPIEngineError(\"QCEngineAPI computation did not execute correctly. Message: \" +                                                                  
 ret[\"error\"][\"error_message\"])\ngeometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution
 Error:\nTraceback (most recent call last):\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/util.py\", line 114, in
 compute_wrapper\n    yield metadata\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/compute.py\", line 91, in     
 compute\n    output_data = executor.compute(input_data, config)\n  File                                                                                    
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/programs/psi4.py\", line 121, in compute\n    pversion =                  
 parse_version(self.get_version())\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/programs/psi4.py\", line 91, in 
 get_version\n    self.version_cache = safe_version(exc[\"stdout\"].split()[-1])\nIndexError: list index out of range\n\n", "traceback": "Traceback (most   
 recent call last):\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/celery/app/trace.py\", line 451, in trace_task\n    R = 
 retval = fun(*args, **kwargs)\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/celery/app/trace.py\", line 734, in          
 __protected_call__\n    return self.run(*args, **kwargs)\n  File                                                                                           
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/openff/bespokefit/executor/services/qcgenerator/worker.py\", line 132, in          
 compute_torsion_drive\n    return_value = qcengine.compute_procedure(\n  File                                                                              
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/compute.py\", line 149, in compute_procedure\n    return                  
 handle_output_metadata(output_data, metadata, raise_error=raise_error, return_dict=return_dict)\n  File                                                    
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/util.py\", line 177, in handle_output_metadata\n    raise                 
 ValueError(output_fusion[\"error\"][\"error_message\"])\nValueError: TorsionDrive error at 90:\ngeomeTRIC run_json error:\nTraceback (most recent call     
 last):\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/run_json.py\", line 225, in geometric_run_json\n          
 geometric.optimize.Optimize(coords, M, IC, engine, None, params)\n  File                                                                                   
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 1331, in Optimize\n    return                        
 optimizer.optimizeGeometry()\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 1293, in        
 optimizeGeometry\n    self.calcEnergyForce()\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 
 1002, in calcEnergyForce\n    spcalc = self.engine.calc(self.X, self.dirname)\n  File                                                                      
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/engine.py\", line 873, in calc\n    return self.calc_new(coords,         
 dirname)\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/engine.py\", line 865, in calc_new\n    raise           
 QCEngineAPIEngineError(\"QCEngineAPI computation did not execute correctly. Message: \" +                                                                  
 ret[\"error\"][\"error_message\"])\ngeometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution
 Error:\nTraceback (most recent call last):\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/util.py\", line 114, in
 compute_wrapper\n    yield metadata\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/compute.py\", line 91, in     
 compute\n    output_data = executor.compute(input_data, config)\n  File                                                                                    
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/programs/psi4.py\", line 121, in compute\n    pversion =                  
 parse_version(self.get_version())\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/programs/psi4.py\", line 91, in 
 get_version\n    self.version_cache = safe_version(exc[\"stdout\"].split()[-1])\nIndexError: list index out of range\n\n\n"}, {"type": "ValueError",       
 "message": "TorsionDrive error at 0:\ngeomeTRIC run_json error:\nTraceback (most recent call last):\n  File                                                
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/run_json.py\", line 225, in geometric_run_json\n                         
 geometric.optimize.Optimize(coords, M, IC, engine, None, params)\n  File                                                                                   
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 1331, in Optimize\n    return                        
 optimizer.optimizeGeometry()\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 1293, in        
 optimizeGeometry\n    self.calcEnergyForce()\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 
 1002, in calcEnergyForce\n    spcalc = self.engine.calc(self.X, self.dirname)\n  File                                                                      
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/engine.py\", line 873, in calc\n    return self.calc_new(coords,         
 dirname)\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/engine.py\", line 865, in calc_new\n    raise           
 QCEngineAPIEngineError(\"QCEngineAPI computation did not execute correctly. Message: \" +                                                                  
 ret[\"error\"][\"error_message\"])\ngeometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution
 Error:\nTraceback (most recent call last):\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/util.py\", line 114, in
 compute_wrapper\n    yield metadata\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/compute.py\", line 91, in     
 compute\n    output_data = executor.compute(input_data, config)\n  File                                                                                    
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/programs/psi4.py\", line 121, in compute\n    pversion =                  
 parse_version(self.get_version())\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/programs/psi4.py\", line 91, in 
 get_version\n    self.version_cache = safe_version(exc[\"stdout\"].split()[-1])\nIndexError: list index out of range\n\n", "traceback": "Traceback (most   
 recent call last):\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/celery/app/trace.py\", line 451, in trace_task\n    R = 
 retval = fun(*args, **kwargs)\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/celery/app/trace.py\", line 734, in          
 __protected_call__\n    return self.run(*args, **kwargs)\n  File                                                                                           
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/openff/bespokefit/executor/services/qcgenerator/worker.py\", line 132, in          
 compute_torsion_drive\n    return_value = qcengine.compute_procedure(\n  File                                                                              
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/compute.py\", line 149, in compute_procedure\n    return                  
 handle_output_metadata(output_data, metadata, raise_error=raise_error, return_dict=return_dict)\n  File                                                    
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/util.py\", line 177, in handle_output_metadata\n    raise                 
 ValueError(output_fusion[\"error\"][\"error_message\"])\nValueError: TorsionDrive error at 0:\ngeomeTRIC run_json error:\nTraceback (most recent call      
 last):\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/run_json.py\", line 225, in geometric_run_json\n          
 geometric.optimize.Optimize(coords, M, IC, engine, None, params)\n  File                                                                                   
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 1331, in Optimize\n    return                        
 optimizer.optimizeGeometry()\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 1293, in        
 optimizeGeometry\n    self.calcEnergyForce()\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 
 1002, in calcEnergyForce\n    spcalc = self.engine.calc(self.X, self.dirname)\n  File                                                                      
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/engine.py\", line 873, in calc\n    return self.calc_new(coords,         
 dirname)\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/engine.py\", line 865, in calc_new\n    raise           
 QCEngineAPIEngineError(\"QCEngineAPI computation did not execute correctly. Message: \" +                                                                  
 ret[\"error\"][\"error_message\"])\ngeometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution
 Error:\nTraceback (most recent call last):\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/util.py\", line 114, in
 compute_wrapper\n    yield metadata\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/compute.py\", line 91, in     
 compute\n    output_data = executor.compute(input_data, config)\n  File                                                                                    
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/programs/psi4.py\", line 121, in compute\n    pversion =                  
 parse_version(self.get_version())\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/programs/psi4.py\", line 91, in 
 get_version\n    self.version_cache = safe_version(exc[\"stdout\"].split()[-1])\nIndexError: list index out of range\n\n\n"}, {"type": "ValueError",       
 "message": "TorsionDrive error at 0:\ngeomeTRIC run_json error:\nTraceback (most recent call last):\n  File                                                
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/run_json.py\", line 225, in geometric_run_json\n                         
 geometric.optimize.Optimize(coords, M, IC, engine, None, params)\n  File                                                                                   
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 1331, in Optimize\n    return                        
 optimizer.optimizeGeometry()\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 1293, in        
 optimizeGeometry\n    self.calcEnergyForce()\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 
 1002, in calcEnergyForce\n    spcalc = self.engine.calc(self.X, self.dirname)\n  File                                                                      
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/engine.py\", line 873, in calc\n    return self.calc_new(coords,         
 dirname)\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/engine.py\", line 865, in calc_new\n    raise           
 QCEngineAPIEngineError(\"QCEngineAPI computation did not execute correctly. Message: \" +                                                                  
 ret[\"error\"][\"error_message\"])\ngeometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution
 Error:\nTraceback (most recent call last):\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/util.py\", line 114, in
 compute_wrapper\n    yield metadata\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/compute.py\", line 91, in     
 compute\n    output_data = executor.compute(input_data, config)\n  File                                                                                    
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/programs/psi4.py\", line 121, in compute\n    pversion =                  
 parse_version(self.get_version())\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/programs/psi4.py\", line 91, in 
 get_version\n    self.version_cache = safe_version(exc[\"stdout\"].split()[-1])\nIndexError: list index out of range\n\n", "traceback": "Traceback (most   
 recent call last):\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/celery/app/trace.py\", line 451, in trace_task\n    R = 
 retval = fun(*args, **kwargs)\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/celery/app/trace.py\", line 734, in          
 __protected_call__\n    return self.run(*args, **kwargs)\n  File                                                                                           
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/openff/bespokefit/executor/services/qcgenerator/worker.py\", line 132, in          
 compute_torsion_drive\n    return_value = qcengine.compute_procedure(\n  File                                                                              
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/compute.py\", line 149, in compute_procedure\n    return                  
 handle_output_metadata(output_data, metadata, raise_error=raise_error, return_dict=return_dict)\n  File                                                    
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/util.py\", line 177, in handle_output_metadata\n    raise                 
 ValueError(output_fusion[\"error\"][\"error_message\"])\nValueError: TorsionDrive error at 0:\ngeomeTRIC run_json error:\nTraceback (most recent call      
 last):\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/run_json.py\", line 225, in geometric_run_json\n          
 geometric.optimize.Optimize(coords, M, IC, engine, None, params)\n  File                                                                                   
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 1331, in Optimize\n    return                        
 optimizer.optimizeGeometry()\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 1293, in        
 optimizeGeometry\n    self.calcEnergyForce()\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 
 1002, in calcEnergyForce\n    spcalc = self.engine.calc(self.X, self.dirname)\n  File                                                                      
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/engine.py\", line 873, in calc\n    return self.calc_new(coords,         
 dirname)\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/engine.py\", line 865, in calc_new\n    raise           
 QCEngineAPIEngineError(\"QCEngineAPI computation did not execute correctly. Message: \" +                                                                  
 ret[\"error\"][\"error_message\"])\ngeometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution
 Error:\nTraceback (most recent call last):\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/util.py\", line 114, in
 compute_wrapper\n    yield metadata\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/compute.py\", line 91, in     
 compute\n    output_data = executor.compute(input_data, config)\n  File                                                                                    
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/programs/psi4.py\", line 121, in compute\n    pversion =                  
 parse_version(self.get_version())\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/programs/psi4.py\", line 91, in 
 get_version\n    self.version_cache = safe_version(exc[\"stdout\"].split()[-1])\nIndexError: list index out of range\n\n\n"}, {"type": "ValueError",       
 "message": "TorsionDrive error at 0:\ngeomeTRIC run_json error:\nTraceback (most recent call last):\n  File                                                
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/run_json.py\", line 225, in geometric_run_json\n                         
 geometric.optimize.Optimize(coords, M, IC, engine, None, params)\n  File                                                                                   
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 1331, in Optimize\n    return                        
 optimizer.optimizeGeometry()\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 1293, in        
 optimizeGeometry\n    self.calcEnergyForce()\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 
 1002, in calcEnergyForce\n    spcalc = self.engine.calc(self.X, self.dirname)\n  File                                                                      
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/engine.py\", line 873, in calc\n    return self.calc_new(coords,         
 dirname)\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/engine.py\", line 865, in calc_new\n    raise           
 QCEngineAPIEngineError(\"QCEngineAPI computation did not execute correctly. Message: \" +                                                                  
 ret[\"error\"][\"error_message\"])\ngeometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution
 Error:\nTraceback (most recent call last):\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/util.py\", line 114, in
 compute_wrapper\n    yield metadata\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/compute.py\", line 91, in     
 compute\n    output_data = executor.compute(input_data, config)\n  File                                                                                    
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/programs/psi4.py\", line 121, in compute\n    pversion =                  
 parse_version(self.get_version())\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/programs/psi4.py\", line 91, in 
 get_version\n    self.version_cache = safe_version(exc[\"stdout\"].split()[-1])\nIndexError: list index out of range\n\n", "traceback": "Traceback (most   
 recent call last):\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/celery/app/trace.py\", line 451, in trace_task\n    R = 
 retval = fun(*args, **kwargs)\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/celery/app/trace.py\", line 734, in          
 __protected_call__\n    return self.run(*args, **kwargs)\n  File                                                                                           
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/openff/bespokefit/executor/services/qcgenerator/worker.py\", line 132, in          
 compute_torsion_drive\n    return_value = qcengine.compute_procedure(\n  File                                                                              
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/compute.py\", line 149, in compute_procedure\n    return                  
 handle_output_metadata(output_data, metadata, raise_error=raise_error, return_dict=return_dict)\n  File                                                    
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/util.py\", line 177, in handle_output_metadata\n    raise                 
 ValueError(output_fusion[\"error\"][\"error_message\"])\nValueError: TorsionDrive error at 0:\ngeomeTRIC run_json error:\nTraceback (most recent call      
 last):\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/run_json.py\", line 225, in geometric_run_json\n          
 geometric.optimize.Optimize(coords, M, IC, engine, None, params)\n  File                                                                                   
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 1331, in Optimize\n    return                        
 optimizer.optimizeGeometry()\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 1293, in        
 optimizeGeometry\n    self.calcEnergyForce()\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/optimize.py\", line 
 1002, in calcEnergyForce\n    spcalc = self.engine.calc(self.X, self.dirname)\n  File                                                                      
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/engine.py\", line 873, in calc\n    return self.calc_new(coords,         
 dirname)\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/geometric/engine.py\", line 865, in calc_new\n    raise           
 QCEngineAPIEngineError(\"QCEngineAPI computation did not execute correctly. Message: \" +                                                                  
 ret[\"error\"][\"error_message\"])\ngeometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution
 Error:\nTraceback (most recent call last):\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/util.py\", line 114, in
 compute_wrapper\n    yield metadata\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/compute.py\", line 91, in     
 compute\n    output_data = executor.compute(input_data, config)\n  File                                                                                    
 \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/programs/psi4.py\", line 121, in compute\n    pversion =                  
 parse_version(self.get_version())\n  File \"/home/ec2-user/miniconda3/envs/bespokefit/lib/python3.9/site-packages/qcengine/programs/psi4.py\", line 91, in 
 get_version\n    self.version_cache = safe_version(exc[\"stdout\"].split()[-1])\nIndexError: list index out of range\n\n\n"}]                              
                                                                                                                                                            
outputs have been saved to acetaminophen.json                                                                                                               
                                                                                                                                                            

worker: Warm shutdown (MainProcess)

worker: Warm shutdown (MainProcess)

worker: Warm shutdown (MainProcess)
@jthorton
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jthorton commented Apr 4, 2022

Hi @xiki-tempula, thanks for making the issue and providing the output! It looks like there may be an issue with your psi4 installation, can you try running psi4 -V in the same conda environment from the command line? If you get the same error then this should confirm an issue with psi4. Note that the default workflow uses psi4 for the QM reference data generation but this can be changed via the command line to use something else like the semi-empirical XTB method for example. To confirm bespokefit is working as expected you could try this, first install it with conda install xtb-python -c conda-forge and then add the following to your run command --default-qc-spec xtb gfn2xtb none which will change the QM reference to the gfn2xtb model.

@xiki-tempula
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@jthorton Thanks. It seems that this is a psi4 issue. It is a bit weird that the conda installed psi4 doesn't work.
I wonder say if I wish to use xtb, what is the optimal setup for a 16 core CPU machine? I wonder if I could just use --n-qc-compute-workers 2 --qc-compute-n-cores 8? Thanks.

@xiki-tempula
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@jthorton I wonder if there is ANI option as well? Thanks.

@jthorton
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jthorton commented Apr 5, 2022

It is a bit weird that the conda installed psi4 doesn't work

This seems to happen if you use conda-forge when solving the psi4 environment rather than the defaults channel I have found it best to make a psi4 environment first and check this works and then install bespokefit after.

I wonder if I could just use --n-qc-compute-workers 2 --qc-compute-n-cores 8? Thanks.

We use QCEngine to run xtb and unfortunately xtb does not respect the number of cores you allocated via QCEngine see my issue for more details, note that it does respect the environment variable OMP_NUM_THREADS which can be used to control the number of cores. For most cases, we have found 1 CPU to be fast enough when using xtb.

I wonder if there is ANI option as well? Thanks.

Of course as we use QCEngine to do our QC reference generation you can use any supported package, however with ANI we often hit geometry optimisation convergence issues in testing but you are welcome to try yourself just add the following to your run command --default-qc-spec torchani ani2x none

@xiki-tempula
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Thanks.

@xiki-tempula xiki-tempula mentioned this issue Apr 21, 2022
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@xiki-tempula @jthorton