kyleabeauchamp
commented
10 years ago I think this is somewhat normal. On Jun 12, 2014 6:35 AM, "monstrouspaddling" notifications@github.com wrote:
CalculateImpliedTimscales.py gives errors when running on Tutorial data. Digging into the code, the error stems from MSMLib.py class Reversible_MLE_Estimator. The logger at line 1238 in MSMLib.py throws the error.
Looking into the scipy.optimize.fmin_l_bfgs_b, the error code 2 is associated with an error in the task: ABNORMAL_TERMINATION_IN_LNSRCH.
Is this a bug, or can these be safely ignored without affecting the output? If it can be ignored, what values can I use to check this - The number of times BFGS is called? The difference between the initial and final log likelihoods?
Thanks!
A log of the output is below:
msmb CalculateImpliedTimescales -l 1,25 -i 1 -o Data/ImpliedTimescales.dat
{'assignments': 'Data/Assignments.h5', 'eigvals': 10, 'interval': 1, 'lagtime': '1,25', 'notrim': False, 'output': 'Data/ImpliedTimescales.dat', 'procs': 1, 'quiet': False, 'symmetrize': 'MLE'} 11:18:06 - Getting 10 eigenvalues (timescales) for each lagtime... 11:18:06 - Building MSMs at the following lag times: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] 11:18:07 - Calculating implied timescales at lagtime 1 11:18:07 - Selected component 0 with population 1.000000 11:18:07 - BFGS likelihood maximization terminated after 179 function calls. Initial and final log likelihoods: -139753.326799, -139753.280195. 11:18:07 - Calculating implied timescales at lagtime 2 11:18:07 - Selected component 0 with population 1.000000 11:18:08 - BFGS likelihood maximization terminated after 290 function calls. Initial and final log likelihoods: -151179.602729, -151179.513937. 11:18:08 - Abnormal termination of BFGS likelihood maximization. Error code 2 11:18:08 - Calculating implied timescales at lagtime 3 11:18:08 - Selected component 0 with population 1.000000 11:18:09 - BFGS likelihood maximization terminated after 208 function calls. Initial and final log likelihoods: -156015.822473, -156015.714189. 11:18:09 - Calculating implied timescales at lagtime 4 11:18:09 - Selected component 0 with population 1.000000 11:18:09 - BFGS likelihood maximization terminated after 150 function calls. Initial and final log likelihoods: -158668.090860, -158667.975200. 11:18:09 - Calculating implied timescales at lagtime 5 11:18:09 - Selected component 0 with population 1.000000 11:18:10 - BFGS likelihood maximization terminated after 159 function calls. Initial and final log likelihoods: -160284.118258, -160283.984699. 11:18:10 - Calculating implied timescales at lagtime 6 11:18:10 - Selected component 0 with population 1.000000 11:18:10 - BFGS likelihood maximization terminated after 191 function calls. Initial and final log likelihoods: -161379.312536, -161379.210149. 11:18:10 - Abnormal termination of BFGS likelihood maximization. Error code 2 11:18:10 - Calculating implied timescales at lagtime 7 11:18:10 - Selected component 0 with population 1.000000 11:18:11 - BFGS likelihood maximization terminated after 214 function calls. Initial and final log likelihoods: -162231.657654, -162231.542798. 11:18:11 - Abnormal termination of BFGS likelihood maximization. Error code 2 11:18:11 - Calculating implied timescales at lagtime 8 11:18:11 - Selected component 0 with population 1.000000 11:18:12 - BFGS likelihood maximization terminated after 225 function calls. Initial and final log likelihoods: -162866.406582, -162866.266906. 11:18:12 - Abnormal termination of BFGS likelihood maximization. Error code 2 11:18:12 - Calculating implied timescales at lagtime 9 11:18:12 - Selected component 0 with population 1.000000 11:18:12 - BFGS likelihood maximization terminated after 168 function calls. Initial and final log likelihoods: -163313.274829, -163313.109101. 11:18:12 - Calculating implied timescales at lagtime 10 11:18:12 - Selected component 0 with population 1.000000 11:18:13 - BFGS likelihood maximization terminated after 142 function calls. Initial and final log likelihoods: -163667.316070, -163667.133324. 11:18:13 - Calculating implied timescales at lagtime 11 11:18:13 - Selected component 0 with population 1.000000 11:18:13 - BFGS likelihood maximization terminated after 159 function calls. Initial and final log likelihoods: -163864.187442, -163863.978430. 11:18:13 - Calculating implied timescales at lagtime 12 11:18:13 - Selected component 0 with population 1.000000 11:18:14 - BFGS likelihood maximization terminated after 145 function calls. Initial and final log likelihoods: -164045.527258, -164045.308630. 11:18:14 - Calculating implied timescales at lagtime 13 11:18:14 - Selected component 0 with population 1.000000 11:18:14 - BFGS likelihood maximization terminated after 227 function calls. Initial and final log likelihoods: -164161.629676, -164161.388940. 11:18:14 - Abnormal termination of BFGS likelihood maximization. Error code 2 11:18:14 - Calculating implied timescales at lagtime 14 11:18:14 - Selected component 0 with population 1.000000 11:18:15 - BFGS likelihood maximization terminated after 141 function calls. Initial and final log likelihoods: -164182.820106, -164182.553320. 11:18:15 - Calculating implied timescales at lagtime 15 11:18:15 - Selected component 0 with population 1.000000 11:18:15 - BFGS likelihood maximization terminated after 201 function calls. Initial and final log likelihoods: -164155.829783, -164155.516090. 11:18:15 - Abnormal termination of BFGS likelihood maximization. Error code 2 11:18:16 - Calculating implied timescales at lagtime 16 11:18:16 - Selected component 0 with population 1.000000 11:18:16 - BFGS likelihood maximization terminated after 206 function calls. Initial and final log likelihoods: -164079.151689, -164078.802164. 11:18:16 - Abnormal termination of BFGS likelihood maximization. Error code 2 11:18:16 - Calculating implied timescales at lagtime 17 11:18:16 - Selected component 0 with population 1.000000 11:18:17 - BFGS likelihood maximization terminated after 149 function calls. Initial and final log likelihoods: -163928.442116, -163928.041659. 11:18:17 - Calculating implied timescales at lagtime 18 11:18:17 - Selected component 0 with population 1.000000 11:18:17 - BFGS likelihood maximization terminated after 146 function calls. Initial and final log likelihoods: -163770.627190, -163770.173608. 11:18:17 - Calculating implied timescales at lagtime 19 11:18:17 - Selected component 0 with population 1.000000 11:18:18 - BFGS likelihood maximization terminated after 198 function calls. Initial and final log likelihoods: -163601.944893, -163601.485538. 11:18:18 - Calculating implied timescales at lagtime 20 11:18:18 - Selected component 0 with population 1.000000 11:18:18 - BFGS likelihood maximization terminated after 195 function calls. Initial and final log likelihoods: -163386.614756, -163386.108368. 11:18:18 - Abnormal termination of BFGS likelihood maximization. Error code 2 11:18:18 - Calculating implied timescales at lagtime 21 11:18:18 - Selected component 0 with population 1.000000 11:18:19 - BFGS likelihood maximization terminated after 187 function calls. Initial and final log likelihoods: -163209.905438, -163209.364213. 11:18:19 - Abnormal termination of BFGS likelihood maximization. Error code 2 11:18:19 - Calculating implied timescales at lagtime 22 11:18:19 - Selected component 0 with population 1.000000 11:18:20 - BFGS likelihood maximization terminated after 146 function calls. Initial and final log likelihoods: -163004.085613, -163003.454112. 11:18:20 - Calculating implied timescales at lagtime 23 11:18:20 - Selected component 0 with population 1.000000 11:18:20 - BFGS likelihood maximization terminated after 194 function calls. Initial and final log likelihoods: -162746.629915, -162745.948430. 11:18:20 - Abnormal termination of BFGS likelihood maximization. Error code 2 11:18:20 - Calculating implied timescales at lagtime 24 11:18:20 - Selected component 0 with population 1.000000 11:18:21 - BFGS likelihood maximization terminated after 147 function calls. Initial and final log likelihoods: -162472.918951, -162472.180937. 11:18:21 - Calculating implied timescales at lagtime 25 11:18:21 - Selected component 0 with population 1.000000 11:18:21 - BFGS likelihood maximization terminated after 204 function calls. Initial and final log likelihoods: -162201.056782, -162200.278590. 11:18:21 - Abnormal termination of BFGS likelihood maximization. Error code 2 11:18:21 - Saved output to Data/ImpliedTimescales.dat
— Reply to this email directly or view it on GitHub https://github.com/SimTk/msmbuilder/issues/425.
davidshorthouse
CalculateImpliedTimscales.py gives errors when running on Tutorial data. Digging into the code, the error stems from MSMLib.py class Reversible_MLE_Estimator. The logger at line 1238 in MSMLib.py throws the error.
Looking into the scipy.optimize.fmin_l_bfgs_b, the error code 2 is associated with an error in the task: ABNORMAL_TERMINATION_IN_LNSRCH.
Is this a bug, or can these be safely ignored without affecting the output? If it can be ignored, what values can I use to check this - The number of times BFGS is called? The difference between the initial and final log likelihoods?
Thanks!
A log of the output is below:
msmb CalculateImpliedTimescales -l 1,25 -i 1 -o Data/ImpliedTimescales.dat
{'assignments': 'Data/Assignments.h5', 'eigvals': 10, 'interval': 1, 'lagtime': '1,25', 'notrim': False, 'output': 'Data/ImpliedTimescales.dat', 'procs': 1, 'quiet': False, 'symmetrize': 'MLE'} 11:18:06 - Getting 10 eigenvalues (timescales) for each lagtime... 11:18:06 - Building MSMs at the following lag times: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] 11:18:07 - Calculating implied timescales at lagtime 1 11:18:07 - Selected component 0 with population 1.000000 11:18:07 - BFGS likelihood maximization terminated after 179 function calls. Initial and final log likelihoods: -139753.326799, -139753.280195. 11:18:07 - Calculating implied timescales at lagtime 2 11:18:07 - Selected component 0 with population 1.000000 11:18:08 - BFGS likelihood maximization terminated after 290 function calls. Initial and final log likelihoods: -151179.602729, -151179.513937. 11:18:08 - Abnormal termination of BFGS likelihood maximization. Error code 2 11:18:08 - Calculating implied timescales at lagtime 3 11:18:08 - Selected component 0 with population 1.000000 11:18:09 - BFGS likelihood maximization terminated after 208 function calls. Initial and final log likelihoods: -156015.822473, -156015.714189. 11:18:09 - Calculating implied timescales at lagtime 4 11:18:09 - Selected component 0 with population 1.000000 11:18:09 - BFGS likelihood maximization terminated after 150 function calls. Initial and final log likelihoods: -158668.090860, -158667.975200. 11:18:09 - Calculating implied timescales at lagtime 5 11:18:09 - Selected component 0 with population 1.000000 11:18:10 - BFGS likelihood maximization terminated after 159 function calls. Initial and final log likelihoods: -160284.118258, -160283.984699. 11:18:10 - Calculating implied timescales at lagtime 6 11:18:10 - Selected component 0 with population 1.000000 11:18:10 - BFGS likelihood maximization terminated after 191 function calls. Initial and final log likelihoods: -161379.312536, -161379.210149. 11:18:10 - Abnormal termination of BFGS likelihood maximization. Error code 2 11:18:10 - Calculating implied timescales at lagtime 7 11:18:10 - Selected component 0 with population 1.000000 11:18:11 - BFGS likelihood maximization terminated after 214 function calls. Initial and final log likelihoods: -162231.657654, -162231.542798. 11:18:11 - Abnormal termination of BFGS likelihood maximization. Error code 2 11:18:11 - Calculating implied timescales at lagtime 8 11:18:11 - Selected component 0 with population 1.000000 11:18:12 - BFGS likelihood maximization terminated after 225 function calls. Initial and final log likelihoods: -162866.406582, -162866.266906. 11:18:12 - Abnormal termination of BFGS likelihood maximization. Error code 2 11:18:12 - Calculating implied timescales at lagtime 9 11:18:12 - Selected component 0 with population 1.000000 11:18:12 - BFGS likelihood maximization terminated after 168 function calls. Initial and final log likelihoods: -163313.274829, -163313.109101. 11:18:12 - Calculating implied timescales at lagtime 10 11:18:12 - Selected component 0 with population 1.000000 11:18:13 - BFGS likelihood maximization terminated after 142 function calls. Initial and final log likelihoods: -163667.316070, -163667.133324. 11:18:13 - Calculating implied timescales at lagtime 11 11:18:13 - Selected component 0 with population 1.000000 11:18:13 - BFGS likelihood maximization terminated after 159 function calls. Initial and final log likelihoods: -163864.187442, -163863.978430. 11:18:13 - Calculating implied timescales at lagtime 12 11:18:13 - Selected component 0 with population 1.000000 11:18:14 - BFGS likelihood maximization terminated after 145 function calls. Initial and final log likelihoods: -164045.527258, -164045.308630. 11:18:14 - Calculating implied timescales at lagtime 13 11:18:14 - Selected component 0 with population 1.000000 11:18:14 - BFGS likelihood maximization terminated after 227 function calls. Initial and final log likelihoods: -164161.629676, -164161.388940. 11:18:14 - Abnormal termination of BFGS likelihood maximization. Error code 2 11:18:14 - Calculating implied timescales at lagtime 14 11:18:14 - Selected component 0 with population 1.000000 11:18:15 - BFGS likelihood maximization terminated after 141 function calls. Initial and final log likelihoods: -164182.820106, -164182.553320. 11:18:15 - Calculating implied timescales at lagtime 15 11:18:15 - Selected component 0 with population 1.000000 11:18:15 - BFGS likelihood maximization terminated after 201 function calls. Initial and final log likelihoods: -164155.829783, -164155.516090. 11:18:15 - Abnormal termination of BFGS likelihood maximization. Error code 2 11:18:16 - Calculating implied timescales at lagtime 16 11:18:16 - Selected component 0 with population 1.000000 11:18:16 - BFGS likelihood maximization terminated after 206 function calls. Initial and final log likelihoods: -164079.151689, -164078.802164. 11:18:16 - Abnormal termination of BFGS likelihood maximization. Error code 2 11:18:16 - Calculating implied timescales at lagtime 17 11:18:16 - Selected component 0 with population 1.000000 11:18:17 - BFGS likelihood maximization terminated after 149 function calls. Initial and final log likelihoods: -163928.442116, -163928.041659. 11:18:17 - Calculating implied timescales at lagtime 18 11:18:17 - Selected component 0 with population 1.000000 11:18:17 - BFGS likelihood maximization terminated after 146 function calls. Initial and final log likelihoods: -163770.627190, -163770.173608. 11:18:17 - Calculating implied timescales at lagtime 19 11:18:17 - Selected component 0 with population 1.000000 11:18:18 - BFGS likelihood maximization terminated after 198 function calls. Initial and final log likelihoods: -163601.944893, -163601.485538. 11:18:18 - Calculating implied timescales at lagtime 20 11:18:18 - Selected component 0 with population 1.000000 11:18:18 - BFGS likelihood maximization terminated after 195 function calls. Initial and final log likelihoods: -163386.614756, -163386.108368. 11:18:18 - Abnormal termination of BFGS likelihood maximization. Error code 2 11:18:18 - Calculating implied timescales at lagtime 21 11:18:18 - Selected component 0 with population 1.000000 11:18:19 - BFGS likelihood maximization terminated after 187 function calls. Initial and final log likelihoods: -163209.905438, -163209.364213. 11:18:19 - Abnormal termination of BFGS likelihood maximization. Error code 2 11:18:19 - Calculating implied timescales at lagtime 22 11:18:19 - Selected component 0 with population 1.000000 11:18:20 - BFGS likelihood maximization terminated after 146 function calls. Initial and final log likelihoods: -163004.085613, -163003.454112. 11:18:20 - Calculating implied timescales at lagtime 23 11:18:20 - Selected component 0 with population 1.000000 11:18:20 - BFGS likelihood maximization terminated after 194 function calls. Initial and final log likelihoods: -162746.629915, -162745.948430. 11:18:20 - Abnormal termination of BFGS likelihood maximization. Error code 2 11:18:20 - Calculating implied timescales at lagtime 24 11:18:20 - Selected component 0 with population 1.000000 11:18:21 - BFGS likelihood maximization terminated after 147 function calls. Initial and final log likelihoods: -162472.918951, -162472.180937. 11:18:21 - Calculating implied timescales at lagtime 25 11:18:21 - Selected component 0 with population 1.000000 11:18:21 - BFGS likelihood maximization terminated after 204 function calls. Initial and final log likelihoods: -162201.056782, -162200.278590. 11:18:21 - Abnormal termination of BFGS likelihood maximization. Error code 2 11:18:21 - Saved output to Data/ImpliedTimescales.dat