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This repository has been archived by the owner on Sep 11, 2023. It is now read-only.
Hi, when I follow the jupyter notebook tutorials, I got no return after a very long time in estimating implied timescales from discrete trajectories at the section of MSM estimation and validation ( Case 2 ). Then I have to press ctrl + C and the trace back show below:
KeyboardInterrupt Traceback (most recent call last)
Cell In [6], line 1
----> 1 its = pyemma.msm.its(cluster.dtrajs, lags=[1, 2, 5, 10, 20, 50], nits=4, errors='bayes')
File ~/miniconda3/envs/pyemma/lib/python3.10/site-packages/pyemma/msm/api.py:253, in timescales_msm(dtrajs, lags, nits, reversible, connected, weights, errors, nsamples, n_jobs, show_progress, mincount_connectivity, only_timescales, core_set, milestoning_method)
250 # go
251 itsobj = _ImpliedTimescales(estimator, lags=lags, nits=nits, n_jobs=n_jobs,
252 show_progress=show_progress, only_timescales=only_timescales)
--> 253 itsobj.estimate(dtrajs)
254 return itsobj
File ~/miniconda3/envs/pyemma/lib/python3.10/site-packages/pyemma/msm/estimators/implied_timescales.py:170, in ImpliedTimescales.estimate(self, X, **params)
147 def estimate(self, X, **params):
148 """
149 Parameters
150 ----------
(...)
168 how many subprocesses to start to estimate the models for each lag time.
169 """
--> 170 return super(ImpliedTimescales, self).estimate(X, **params)
File ~/miniconda3/envs/pyemma/lib/python3.10/site-packages/pyemma/_base/estimator.py:418, in Estimator.estimate(self, X, **params)
416 if params:
417 self.set_params(**params)
--> 418 self._model = self._estimate(X)
419 # ensure _estimate returned something
420 assert self._model is not None
File ~/miniconda3/envs/pyemma/lib/python3.10/site-packages/pyemma/msm/estimators/implied_timescales.py:235, in ImpliedTimescales._estimate(self, dtrajs)
233 with ctx:
234 if not self.only_timescales:
--> 235 models, estimators = estimate_param_scan(self.estimator, dtrajs, param_sets, failfast=False,
236 return_estimators=True, n_jobs=self.n_jobs,
237 progress_reporter=pg, return_exceptions=True)
238 self._estimators = estimators
239 else:
File ~/miniconda3/envs/pyemma/lib/python3.10/site-packages/pyemma/_base/estimator.py:361, in estimate_param_scan(estimator, X, param_sets, evaluate, evaluate_args, failfast, return_estimators, n_jobs, progress_reporter, show_progress, return_exceptions)
358 with closing(pool), ctx:
359 res_async = [pool.apply_async(_estimate_param_scan_worker, a, callback=callback,
360 error_callback=error_callback) for a in args]
--> 361 res = [x.get() for x in res_async]
363 # if n_jobs=1 don't invoke the pool, but directly dispatch the iterator
364 else:
365 if logger_available:
File ~/miniconda3/envs/pyemma/lib/python3.10/site-packages/pyemma/_base/estimator.py:361, in <listcomp>(.0)
358 with closing(pool), ctx:
359 res_async = [pool.apply_async(_estimate_param_scan_worker, a, callback=callback,
360 error_callback=error_callback) for a in args]
--> 361 res = [x.get() for x in res_async]
363 # if n_jobs=1 don't invoke the pool, but directly dispatch the iterator
364 else:
365 if logger_available:
File ~/miniconda3/envs/pyemma/lib/python3.10/site-packages/multiprocess/pool.py:765, in ApplyResult.get(self, timeout)
764 def get(self, timeout=None):
--> 765 self.wait(timeout)
766 if not self.ready():
767 raise TimeoutError
File ~/miniconda3/envs/pyemma/lib/python3.10/site-packages/multiprocess/pool.py:762, in ApplyResult.wait(self, timeout)
761 def wait(self, timeout=None):
--> 762 self._event.wait(timeout)
File ~/miniconda3/envs/pyemma/lib/python3.10/threading.py:607, in Event.wait(self, timeout)
605 signaled = self._flag
606 if not signaled:
--> 607 signaled = self._cond.wait(timeout)
608 return signaled
File ~/miniconda3/envs/pyemma/lib/python3.10/threading.py:320, in Condition.wait(self, timeout)
318 try: # restore state no matter what (e.g., KeyboardInterrupt)
319 if timeout is None:
--> 320 waiter.acquire()
321 gotit = True
322 else:
KeyboardInterrupt:
command history
The full command history is here ( I just copy it from html document):
pdb = mdshare.fetch('alanine-dipeptide-nowater.pdb', working_directory='data')
files = mdshare.fetch('alanine-dipeptide-*-250ns-nowater.xtc', working_directory='data')
feat = pyemma.coordinates.featurizer(pdb)
feat.add_backbone_torsions(periodic=False)
data = pyemma.coordinates.load(files, features=feat)
data_concatenated = np.concatenate(data)
cluster = pyemma.coordinates.cluster_kmeans(data, k=200, max_iter=50, stride=10)
its = pyemma.msm.its(cluster.dtrajs, lags=[1, 2, 5, 10, 20, 50], nits=4, errors='bayes')
Hi, when I follow the jupyter notebook tutorials, I got no return after a very long time in estimating implied timescales from discrete trajectories at the section of MSM estimation and validation ( Case 2 ). Then I have to press ctrl + C and the trace back show below:
The full command history is here ( I just copy it from html document):
pdb = mdshare.fetch('alanine-dipeptide-nowater.pdb', working_directory='data')
files = mdshare.fetch('alanine-dipeptide-*-250ns-nowater.xtc', working_directory='data')
feat = pyemma.coordinates.featurizer(pdb)
feat.add_backbone_torsions(periodic=False)
data = pyemma.coordinates.load(files, features=feat)
data_concatenated = np.concatenate(data)
cluster = pyemma.coordinates.cluster_kmeans(data, k=200, max_iter=50, stride=10)
its = pyemma.msm.its(cluster.dtrajs, lags=[1, 2, 5, 10, 20, 50], nits=4, errors='bayes')
My related environment list here ( I install PyEMMA via conda ):
PyEMMA 2.5.12
numpy 1.23.3
pyemma 2.5.12
mdshare 0.4.2
scipy 1.9.1
IPython : 8.5.0
ipykernel : 6.15.3
ipywidgets : 7.7.2
jupyter_client : 7.3.5
jupyter_core : 4.11.1
jupyter_server : 1.18.1
jupyterlab : 3.4.7
nbclient : 0.6.8
nbconvert : 7.0.0
nbformat : 5.5.0
notebook : 6.4.12
qtconsole : 5.3.2
traitlets : 5.4.0
Python 3.10.6
Any one help me? Thank you!
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