andrrizzi
commented
4 years ago Hi Jiyuan. That message shouldn't be a problem, and you can ignore it.
Closed kingljy0818 closed 4 years ago
andrrizzi
commented
4 years ago Hi Jiyuan. That message shouldn't be a problem, and you can ignore it.
kingljy0818
commented
4 years ago Hi andrrizzi. Although I could ignore the dcdplugin prompt, it was displayed the error information in the follow when I perform the analyze command:
--------------------------------------------------------------------------------------------------------------
(base) [root@localhost t4-lysozyme]# yank analyze --store=LZ02-mertk-explicit-output
Traceback (most recent call last):
File "/home/anaconda3/bin/yank", line 11, in <module>
load_entry_point('yank==0.25.2', 'console_scripts', 'yank')()
File "/home/anaconda3/lib/python3.7/site-packages/yank/cli.py", line 73, in main
dispatched = getattr(commands, command).dispatch(command_args)
File "/home/anaconda3/lib/python3.7/site-packages/yank/commands/analyze.py", line 148, in dispatch
single_run()
File "/home/anaconda3/lib/python3.7/site-packages/mpiplus/mpiplus.py", line 271, in _wrapper
return run_single_node(rank, task, *args, **kwargs)
File "/home/anaconda3/lib/python3.7/site-packages/mpiplus/mpiplus.py", line 220, in run_single_node
result = task(*args, **kwargs)
File "/home/anaconda3/lib/python3.7/site-packages/yank/commands/analyze.py", line 143, in single_run
output = analyze.analyze_directory(args['--store'], **analyzer_kwargs)
File "/home/anaconda3/lib/python3.7/site-packages/yank/analyze.py", line 782, in analyze_directory
auto_experiment_analyzer = ExperimentAnalyzer(source_directory, **analyzer_kwargs)
File "/home/anaconda3/lib/python3.7/site-packages/yank/analyze.py", line 297, in __init__
raise RuntimeError(err_msg)
RuntimeError: Cannot find analysis.yaml script in LZ02-mertk-explicit-output
Exception ignored in: <function ExperimentAnalyzer.__del__ at 0x7fdc0191d200>
Traceback (most recent call last):
File "/home/anaconda3/lib/python3.7/site-packages/yank/analyze.py", line 336, in __del__
for phase, analyzer in self.analyzers.items():
AttributeError: 'ExperimentAnalyzer' object has no attribute 'analyzers'
--------------------------------------------------------------------------------------------------------------I also modified the netcdf file, but it prompted the another error in the follow:
-------------------------------------------------------------------------------------------------------------
(base) [root@localhost t4-lysozyme]# yank analyze --store=LZ02-mertk-explicit-output/experiments
/home/anaconda3/lib/python3.7/site-packages/yank/analyze.py:299: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
analysis = yaml.load(f)
2020-04-09 16:30:50,235: WARNING - openmmtools.multistate.multistatereporter - Warning: The openmmtools.multistate API is experimental and may change in future releases
2020-04-09 16:30:50,274: WARNING - openmmtools.multistate.multistateanalyzer - Warning: The openmmtools.multistate API is experimental and may change in future releases
2020-04-09 16:30:50,277: WARNING - openmmtools.multistate.multistatereporter - Warning: The openmmtools.multistate API is experimental and may change in future releases
2020-04-09 16:30:50,296: WARNING - openmmtools.multistate.multistateanalyzer - Warning: The openmmtools.multistate API is experimental and may change in future releases
WARNING: Did not converge to within specified tolerance.
max_delta = 4.205500e-03, tol = 1.000000e-12, maximum_iterations = 250, iterations completed = 249
Traceback (most recent call last):
File "/home/anaconda3/bin/yank", line 11, in <module>
load_entry_point('yank==0.25.2', 'console_scripts', 'yank')()
File "/home/anaconda3/lib/python3.7/site-packages/yank/cli.py", line 73, in main
dispatched = getattr(commands, command).dispatch(command_args)
File "/home/anaconda3/lib/python3.7/site-packages/yank/commands/analyze.py", line 148, in dispatch
single_run()
File "/home/anaconda3/lib/python3.7/site-packages/mpiplus/mpiplus.py", line 271, in _wrapper
return run_single_node(rank, task, *args, **kwargs)
File "/home/anaconda3/lib/python3.7/site-packages/mpiplus/mpiplus.py", line 220, in run_single_node
result = task(*args, **kwargs)
File "/home/anaconda3/lib/python3.7/site-packages/yank/commands/analyze.py", line 143, in single_run
output = analyze.analyze_directory(args['--store'], **analyzer_kwargs)
File "/home/anaconda3/lib/python3.7/site-packages/yank/analyze.py", line 783, in analyze_directory
analysis_data = auto_experiment_analyzer.auto_analyze()
File "/home/anaconda3/lib/python3.7/site-packages/yank/analyze.py", line 173, in make_copy
return copy.deepcopy(wrap(*args, **kwargs))
File "/home/anaconda3/lib/python3.7/site-packages/yank/analyze.py", line 705, in auto_analyze
_ = self.get_experiment_free_energy_data()
File "/home/anaconda3/lib/python3.7/site-packages/yank/analyze.py", line 173, in make_copy
return copy.deepcopy(wrap(*args, **kwargs))
File "/home/anaconda3/lib/python3.7/site-packages/yank/analyze.py", line 565, in get_experiment_free_energy_data
data[phase_name] = analyzer.analyze_phase()
File "/home/anaconda3/lib/python3.7/site-packages/yank/analyze.py", line 151, in analyze_phase
Deltaf_ij, dDeltaf_ij = self.get_free_energy()
File "/home/anaconda3/lib/python3.7/site-packages/openmmtools/multistate/multistateanalyzer.py", line 1924, in get_free_energy
self._compute_free_energy()
File "/home/anaconda3/lib/python3.7/site-packages/openmmtools/multistate/multistateanalyzer.py", line 1884, in _compute_free_energy
(Deltaf_ij, dDeltaf_ij) = self.mbar.getFreeEnergyDifferences()
File "/home/anaconda3/lib/python3.7/site-packages/pymbar/mbar.py", line 542, in getFreeEnergyDifferences
np.exp(self.Log_W_nk), self.N_k, method=uncertainty_method)
File "/home/anaconda3/lib/python3.7/site-packages/pymbar/mbar.py", line 1679, in _computeAsymptoticCovarianceMatrix
check_w_normalized(W, N_k)
File "/home/anaconda3/lib/python3.7/site-packages/pymbar/utils.py", line 360, in check_w_normalized
(firstbad, column_sums[firstbad], np.sum(badcolumns)))
pymbar.utils.ParameterError: Warning: Should have \sum_n W_nk = 1. Actual column sum for state 0 was 1.259701. 27 other columns have similar problems
--------------------------------------------------------------------------------------------------------------Would need your help to solve this problem. Many thanks.
andrrizzi
commented
4 years ago It looks to me you have an outdated installation. I'd try to update yank and openmmtools.
kingljy0818
commented
4 years ago Dear Andrrizzi. I have solved this problem by searching issues.
kingljy0818
commented
4 years ago In this issue https://github.com/choderalab/yank/issues/1203, downgrading to pymbar 3.0.3 could be solved the error above.
andrrizzi
commented
4 years ago Thanks for posting the solution, @kingljy0818 . I'm glad you made it work.
owenustc
commented
2 years ago hi I have downgrading the pymbar to 3.0.3， but It is also not work， which error message as follow： 2022-01-24 08:50:30,651: Iteration took 3.970s. 2022-01-24 08:50:30,651: Estimated completion in 0:00:00, at Mon Jan 24 08:50:30 2022 (consuming total wall clock time 0:10:44.765272). 2022-01-24 08:50:30,835: Single node: executing <bound method MultiStateReporter.close of <openmmtools.multistate.multistatereporter.MultiStateReporter object at 0x7fbef97615b0>> Please cite the following:
Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, LeGrand S, Beberg AL, Ensign DL, Bruns CM, and Pande VS. Accelerating molecular dynamic simulations on graphics processing unit. J. Comput. Chem. 30:864, 2009. DOI: 10.1002/jcc.21209
Eastman P and Pande VS. OpenMM: A hardware-independent framework for molecular simulations. Comput. Sci. Eng. 12:34, 2010. DOI: 10.1109/MCSE.2010.27
Eastman P and Pande VS. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J. Comput. Chem. 31:1268, 2010. DOI: 10.1002/jcc.21413
Eastman P and Pande VS. Constant constraint matrix approximation: A robust, parallelizable constraint method for molecular simulations. J. Chem. Theor. Comput. 6:434, 2010. DOI: 10.1021/ct900463w
Chodera JD and Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs multistate: Simple improvements for enhanced mixing. J. Chem. Phys., 135:194110, 2011. DOI:10.1063/1.3660669Please cite the following:
Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, LeGrand S, Beberg AL, Ensign DL, Bruns CM, and Pande VS. Accelerating molecular dynamic simulations on graphics processing unit. J. Comput. Chem. 30:864, 2009. DOI: 10.1002/jcc.21209
Eastman P and Pande VS. OpenMM: A hardware-independent framework for molecular simulations. Comput. Sci. Eng. 12:34, 2010. DOI: 10.1109/MCSE.2010.27
Eastman P and Pande VS. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J. Comput. Chem. 31:1268, 2010. DOI: 10.1002/jcc.21413
Eastman P and Pande VS. Constant constraint matrix approximation: A robust, parallelizable constraint method for molecular simulations. J. Chem. Theor. Comput. 6:434, 2010. DOI: 10.1021/ct900463w
Chodera JD and Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs multistate: Simple improvements for enhanced mixing. J. Chem. Phys., 135:194110, 2011. DOI:10.1063/1.3660669dcdplugin) Could not access file 'explicit/experiments/trailblaze/solvent2/coordinates.dcd'.
Analyzing data...
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Traceback (most recent call last):
File "/root/miniconda3/bin/yank", line 33, in
my openmm version is 7.6.0
Dear all,
When the 500 default of iteration was completed, it displayed the error in the follow:
2020-04-08 12:31:04,913: Iteration 500/500 2020-04-08 12:31:04,913: **** 2020-04-08 12:31:04,913: Single node: executing <function ReplicaExchangeSampler._mix_replicas at 0x7f99a233ab00> 2020-04-08 12:31:04,913: Mixing replicas... 2020-04-08 12:31:04,925: Mixing of replicas took 0.012s 2020-04-08 12:31:04,925: Accepted 39952/388962 attempted swaps (10.3%) 2020-04-08 12:31:04,926: Propagating all replicas... 2020-04-08 12:31:04,926: Running _propagate_replica serially. 2020-04-08 12:31:15,251: Running _get_replica_move_statistics serially. 2020-04-08 12:31:15,251: Propagating all replicas took 10.325s 2020-04-08 12:31:15,251: Running _compute_replica_energies serially. 2020-04-08 12:31:15,886: Computing energy matrix took 0.635s 2020-04-08 12:31:15,886: Single node: executing <function MultiStateSampler._report_iteration at 0x7f99a2375170> 2020-04-08 12:31:15,887: Single node: executing <function MultiStateSampler._report_iteration_items at 0x7f99a2375440> 2020-04-08 12:31:15,897: Storing sampler states took 0.010s 2020-04-08 12:31:16,010: Writing iteration information to storage took 0.123s 2020-04-08 12:31:16,010: Will perform offline analysis 2020-04-08 12:31:16,010: Single node: executing <function MultiStateSampler._offline_analysis at 0x7f99a2375d40> 2020-04-08 12:31:16,010: WARNING - openmmtools.multistate.multistateanalyzer - Warning: The openmmtools.multistate API is experimental and may change in future releases 2020-04-08 12:31:16,013: Computing free energy with MBAR... 2020-04-08 12:31:16,013: Checking if we need to unbias the restraint... 2020-04-08 12:31:16,013: Reading energies... 2020-04-08 12:31:16,042: read_replica_thermodynamic_states: iteration = [ 0 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 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500] 2020-04-08 12:31:16,047: Done. 2020-04-08 12:31:16,048: Assembling effective timeseries... 2020-04-08 12:31:16,064: Done. 2020-04-08 12:31:16,064: Could not find t0: None of the requested keys could be found on disk! 2020-04-08 12:31:16,076: Equilibration data: 2020-04-08 12:31:16,077: number of iterations discarded to equilibration : 186 2020-04-08 12:31:16,077: statistical inefficiency of production region : 3.075929880142212 2020-04-08 12:31:16,077: effective number of uncorrelated samples : 102.73316192626953 2020-04-08 12:31:16,077: Assembling uncorrelated energies... 2020-04-08 12:31:16,081: Found expanded cutoff states in the energies! 2020-04-08 12:31:16,081: Free energies will be reported relative to them instead! 2020-04-08 12:31:16,082: Done. 2020-04-08 12:31:16,082: Computing free energy differences... 2020-04-08 12:31:16,085: Computing offline free energy estimate took 0.074s 2020-04-08 12:31:16,085: Iteration took 11.172s. 2020-04-08 12:31:16,085: Estimated completion in 0:00:00, at Wed Apr 8 12:31:16 2020 (consuming total wall clock time 1:32:04.244310). 2020-04-08 12:31:16,569: Single node: executing <bound method MultiStateReporter.close of <openmmtools.multistate.multistatereporter.MultiStateReporter object at 0x7f99958c4d10>> Please cite the following:
Please cite the following:
dcdplugin) Could not access file 'LZ02-mertk-explicit-output/experiments/trailblaze/complex/coordinates.dcd'. dcdplugin) Could not access file 'LZ02-mertk-explicit-output/experiments/trailblaze/solvent/coordinates.dcd'.
Would you help me to solve this problem,many thanks.
Kindest regareds
Jiyuan